rs2477142

Variant names:

• chr1-17302509-C-T
• rs2477142

Variant summary

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

The variant allele was found at a frequency of 0.618 in 152,142 control chromosomes in the GnomAD database, including 29,903 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 0.62 (29903 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 6 publications found

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 = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93849 AN: 152024 Hom.: 29842 Cov.: 34

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.618 AC: 93976 AN: 152142 Hom.: 29903 Cov.: 34 AF XY: 0.614 AC XY: 45646 AN XY: 74366

African (AFR) AF: 0.766 AC: 31807 AN: 41522

American (AMR) AF: 0.578 AC: 8829 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1878 AN: 5178

South Asian (SAS) AF: 0.517 AC: 2491 AN: 4814

European-Finnish (FIN) AF: 0.566 AC: 5986 AN: 10580

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.578 AC: 39293 AN: 67988

Other (OTH) AF: 0.616 AC: 1303 AN: 2114

Alfa AF: 0.591 Hom.: 66498

Bravo AF: 0.624

Asia WGS AF: 0.518 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.82
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2477142; hg19: chr1-17629004;