rs1369276

Variant names:

• chr3-164442850-C-A
• rs1369276

Your query was ambiguous. Multiple possible variants found:

• chr3-164442850-C-A
• chr3-164442850-C-G

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 0.505 in 151,514 control chromosomes in the GnomAD database, including 19,670 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 0.51 (19670 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.505 AC: 76484 AN: 151396 Hom.: 19639 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.505 AC: 76566 AN: 151514 Hom.: 19670 Cov.: 31 AF XY: 0.504 AC XY: 37315 AN XY: 74026

African (AFR) AF: 0.590 AC: 24364 AN: 41320

American (AMR) AF: 0.559 AC: 8485 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1632 AN: 3454

East Asian (EAS) AF: 0.342 AC: 1759 AN: 5138

South Asian (SAS) AF: 0.395 AC: 1904 AN: 4824

European-Finnish (FIN) AF: 0.513 AC: 5403 AN: 10526

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

European-Non Finnish (NFE) AF: 0.464 AC: 31436 AN: 67766

Other (OTH) AF: 0.490 AC: 1029 AN: 2098

Alfa AF: 0.499 Hom.: 3235

Bravo AF: 0.516

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.047
DANN	Benign	0.33
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1369276; hg19: chr3-164160638;