rs61742070

Variant names:

• chr11-101958339-C-T
• rs61742070
• NM_020802.4:c.678C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-101958339-C-T
• chr11-101958339-C-A
• chr11-101958339-C-G

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BS1 BS2

The NM_020802.4(CEP126):​c.678C>T​(p.Leu226Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,613,704 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0096 (27 hom., cov: 32)
  • Exomes 𝑓: 0.00093 (20 hom.)
• Consequence: CEP126 NM_020802.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.226
• Publications: 2 publications found

Genes affected

CEP126 (HGNC:29264): (centrosomal protein 126) Involved in cilium assembly; cytoplasmic microtubule organization; and mitotic spindle organization. Located in centrosome; ciliary base; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BP6: Variant 11-101958339-C-T is Benign according to our data. Variant chr11-101958339-C-T is described in ClinVar as Benign. ClinVar VariationId is 786211.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.226 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00962 (1464/152224) while in subpopulation AFR AF = 0.0338 (1403/41542). AF 95% confidence interval is 0.0323. There are 27 homozygotes in GnomAd4. There are 715 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 27 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020802.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP126	NM_020802.4	MANE Select	c.678C>T	p.Leu226Leu	synonymous	Exon 5 of 11	NP_065853.3	Q9P2H0
	CEP126	NM_001363543.2		c.81C>T	p.Leu27Leu	synonymous	Exon 6 of 12	NP_001350472.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP126	ENST00000263468.13	TSL:1 MANE Select	c.678C>T	p.Leu226Leu	synonymous	Exon 5 of 11	ENSP00000263468.8	Q9P2H0
	CEP126	ENST00000931861.1		c.678C>T	p.Leu226Leu	synonymous	Exon 5 of 11	ENSP00000601920.1
	CEP126	ENST00000532529.1	TSL:5	n.*174C>T		non_coding_transcript_exon	Exon 4 of 10	ENSP00000433643.1	H0YDI0

Frequencies

GnomAD3 genomes AF: 0.00955 AC: 1452 AN: 152106 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00242

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00528

GnomAD2 exomes AF: 0.00233 AC: 584 AN: 250866 AF XY: 0.00174

Gnomad AFR exome AF: 0.0331

Gnomad AMR exome AF: 0.000955

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000123

Gnomad OTH exome AF: 0.000491

GnomAD4 exome AF: 0.000928 AC: 1356 AN: 1461480 Hom.: 20 Cov.: 31 AF XY: 0.000779 AC XY: 566 AN XY: 727024

African (AFR) AF: 0.0327 AC: 1094 AN: 33456

American (AMR) AF: 0.00139 AC: 62 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26124

East Asian (EAS) AF: 0.00 AC: 0 AN: 39646

South Asian (SAS) AF: 0.0000580 AC: 5 AN: 86232

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53374

Middle Eastern (MID) AF: 0.000695 AC: 4 AN: 5752

European-Non Finnish (NFE) AF: 0.0000630 AC: 70 AN: 1111802

Other (OTH) AF: 0.00200 AC: 121 AN: 60374

GnomAD4 genome AF: 0.00962 AC: 1464 AN: 152224 Hom.: 27 Cov.: 32 AF XY: 0.00961 AC XY: 715 AN XY: 74412

African (AFR) AF: 0.0338 AC: 1403 AN: 41542

American (AMR) AF: 0.00242 AC: 37 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10598

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 68004

Other (OTH) AF: 0.00523 AC: 11 AN: 2104

Alfa AF: 0.00317 Hom.: 3

Bravo AF: 0.0104

Asia WGS AF: 0.00115 AC: 4 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.000119

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	6.8
DANN	Benign	0.67
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs61742070; hg19: chr11-101829070;