rs2938844

Variant names:

• chr7-9587289-G-A
• rs2938844

Your query was ambiguous. Multiple possible variants found:

• chr7-9587289-G-A
• chr7-9587289-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 0.357 in 151,850 control chromosomes in the GnomAD database, including 10,252 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 (10252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 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: 0.357 AC: 54113 AN: 151732 Hom.: 10238 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.357 AC: 54148 AN: 151850 Hom.: 10252 Cov.: 32 AF XY: 0.356 AC XY: 26388 AN XY: 74206

African (AFR) AF: 0.264 AC: 10912 AN: 41408

American (AMR) AF: 0.435 AC: 6627 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1407 AN: 3466

East Asian (EAS) AF: 0.172 AC: 886 AN: 5146

South Asian (SAS) AF: 0.436 AC: 2102 AN: 4822

European-Finnish (FIN) AF: 0.342 AC: 3601 AN: 10542

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27170 AN: 67906

Other (OTH) AF: 0.364 AC: 767 AN: 2108

Alfa AF: 0.371 Hom.: 1788

Bravo AF: 0.356

Asia WGS AF: 0.264 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.58
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2938844; hg19: chr7-9626919;