rs2816057

Variant names:

• chr1-18575763-G-C
• rs2816057

Your query was ambiguous. Multiple possible variants found:

• chr1-18575763-G-C
• chr1-18575763-G-T

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 0.446 in 151,966 control chromosomes in the GnomAD database, including 16,691 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 0.45 (16691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67790 AN: 151848 Hom.: 16668 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.446 AC: 67848 AN: 151966 Hom.: 16691 Cov.: 32 AF XY: 0.452 AC XY: 33585 AN XY: 74246

African (AFR) AF: 0.239 AC: 9895 AN: 41472

American (AMR) AF: 0.554 AC: 8459 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1685 AN: 3472

East Asian (EAS) AF: 0.354 AC: 1814 AN: 5124

South Asian (SAS) AF: 0.597 AC: 2873 AN: 4810

European-Finnish (FIN) AF: 0.523 AC: 5519 AN: 10556

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36136 AN: 67944

Other (OTH) AF: 0.470 AC: 994 AN: 2114

Alfa AF: 0.331 Hom.: 927

Bravo AF: 0.437

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.74
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs2816057; hg19: chr1-18902257;