chr1-166321824-T-C

Variant names:

• chr1-166321824-T-C
• rs10918425
• ENST00000653824.3:n.221-13504T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653824.3(ENSG00000229588):​n.221-13504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 152,234 control chromosomes in the GnomAD database, including 1,483 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 0.080 (1483 hom., cov: 32)
• Consequence: ENSG00000229588 ENST00000653824.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 1 publications found

Genes affected

ENSG00000229588 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653824.3. 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
	ENSG00000229588	ENST00000653824.3		n.221-13504T>C		intron	N/A
	ENSG00000229588	ENST00000829274.1		n.179-17076T>C		intron	N/A
	ENSG00000229588	ENST00000829275.1		n.190-13504T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12205 AN: 152116 Hom.: 1475 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00121

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0804 AC: 12243 AN: 152234 Hom.: 1483 Cov.: 32 AF XY: 0.0792 AC XY: 5894 AN XY: 74464

African (AFR) AF: 0.261 AC: 10816 AN: 41482

American (AMR) AF: 0.0507 AC: 775 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3472

East Asian (EAS) AF: 0.0766 AC: 397 AN: 5182

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4826

European-Finnish (FIN) AF: 0.000282 AC: 3 AN: 10628

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

European-Non Finnish (NFE) AF: 0.00121 AC: 82 AN: 68024

Other (OTH) AF: 0.0624 AC: 132 AN: 2114

Alfa AF: 0.0288 Hom.: 192

Bravo AF: 0.0932

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.86
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10918425; hg19: chr1-166291061;