rs2369955

Variant names:

• chr3-132974744-A-C
• rs2369955

Your query was ambiguous. Multiple possible variants found:

• chr3-132974744-A-C
• chr3-132974744-A-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 0.104 in 152,202 control chromosomes in the GnomAD database, including 930 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 0.10 (930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 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: 0.104 AC: 15850 AN: 152084 Hom.: 924 Cov.: 32

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.104 AC: 15872 AN: 152202 Hom.: 930 Cov.: 32 AF XY: 0.106 AC XY: 7876 AN XY: 74412

African (AFR) AF: 0.0541 AC: 2247 AN: 41548

American (AMR) AF: 0.140 AC: 2134 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 288 AN: 3462

East Asian (EAS) AF: 0.142 AC: 736 AN: 5168

South Asian (SAS) AF: 0.103 AC: 494 AN: 4814

European-Finnish (FIN) AF: 0.142 AC: 1507 AN: 10590

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8177 AN: 68016

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.114 Hom.: 1545

Bravo AF: 0.103

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.52
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs2369955; hg19: chr3-132693588;