rs3806318

Variant names:

• chr1-65419674-A-G
• rs3806318

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 0.197 in 152,038 control chromosomes in the GnomAD database, including 3,634 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 0.20 (3634 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475
• Publications: 24 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 (SAS) allele frequency at 95% confidence interval = 0.346 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: 0.197 AC: 29972 AN: 151920 Hom.: 3636 Cov.: 31

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.197 AC: 29967 AN: 152038 Hom.: 3634 Cov.: 31 AF XY: 0.195 AC XY: 14512 AN XY: 74292

African (AFR) AF: 0.0612 AC: 2539 AN: 41492

American (AMR) AF: 0.178 AC: 2724 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3470

East Asian (EAS) AF: 0.126 AC: 652 AN: 5166

South Asian (SAS) AF: 0.360 AC: 1734 AN: 4810

European-Finnish (FIN) AF: 0.189 AC: 1992 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18672 AN: 67952

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.250 Hom.: 9682

Bravo AF: 0.183

Asia WGS AF: 0.204 AC: 709 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	3.4
DANN	Benign	0.76
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3806318; hg19: chr1-65885357;