rs3922812

Variant names:

• chr1-178690798-G-A
• rs3922812

Your query was ambiguous. Multiple possible variants found:

• chr1-178690798-G-A
• chr1-178690798-G-C

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 0.356 in 151,702 control chromosomes in the GnomAD database, including 10,258 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 0.36 (10258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 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: 0.356 AC: 54038 AN: 151582 Hom.: 10248 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.356 AC: 54066 AN: 151702 Hom.: 10258 Cov.: 32 AF XY: 0.354 AC XY: 26208 AN XY: 74126

African (AFR) AF: 0.228 AC: 9382 AN: 41232

American (AMR) AF: 0.433 AC: 6610 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1790 AN: 5158

South Asian (SAS) AF: 0.394 AC: 1895 AN: 4810

European-Finnish (FIN) AF: 0.362 AC: 3815 AN: 10530

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27697 AN: 67934

Other (OTH) AF: 0.378 AC: 800 AN: 2114

Alfa AF: 0.389 Hom.: 38371

Bravo AF: 0.354

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.024
DANN	Benign	0.73
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs3922812; hg19: chr1-178659933;