rs3813627

Variant names:

• chr1-161225358-G-T
• rs3813627

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 0.288 in 152,158 control chromosomes in the GnomAD database, including 7,246 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 0.29 (7246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.288 AC: 43794 AN: 152040 Hom.: 7246 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.288 AC: 43801 AN: 152158 Hom.: 7246 Cov.: 32 AF XY: 0.289 AC XY: 21516 AN XY: 74382

African (AFR) AF: 0.122 AC: 5057 AN: 41522

American (AMR) AF: 0.357 AC: 5458 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2776 AN: 5172

South Asian (SAS) AF: 0.315 AC: 1521 AN: 4832

European-Finnish (FIN) AF: 0.314 AC: 3327 AN: 10586

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23566 AN: 67978

Other (OTH) AF: 0.306 AC: 647 AN: 2116

Alfa AF: 0.336 Hom.: 15066

Bravo AF: 0.285

Asia WGS AF: 0.435 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.74
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs3813627; hg19: chr1-161195148;