2-126316168-T-C

Variant names:

• chr2-126316168-T-C
• rs11679324
• ENST00000419223.3:n.400+3631T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000419223.3(ENSG00000235774):​n.400+3631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 152,326 control chromosomes in the GnomAD database, including 143 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.037 (143 hom., cov: 32)
• Consequence: ENSG00000235774 ENST00000419223.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.936
• Publications: 1 publications found

Genes affected

ENSG00000235774 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419223.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235774	ENST00000419223.3	TSL:5	n.400+3631T>C		intron	N/A
	ENSG00000235774	ENST00000435352.2	TSL:4	n.400+3631T>C		intron	N/A
	ENSG00000235774	ENST00000799479.1		n.389+3631T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5569 AN: 152208 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0358

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0366 AC: 5575 AN: 152326 Hom.: 143 Cov.: 32 AF XY: 0.0369 AC XY: 2750 AN XY: 74490

African (AFR) AF: 0.0590 AC: 2453 AN: 41562

American (AMR) AF: 0.0199 AC: 304 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.00766 AC: 37 AN: 4830

European-Finnish (FIN) AF: 0.0515 AC: 547 AN: 10622

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0308 AC: 2094 AN: 68028

Other (OTH) AF: 0.0354 AC: 75 AN: 2116

Alfa AF: 0.0236 Hom.: 12

Bravo AF: 0.0351

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.87
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs11679324; hg19: chr2-127073745;