rs7958592

Variant names:

• chr12-23354842-G-A
• rs7958592

Your query was ambiguous. Multiple possible variants found:

• chr12-23354842-G-A
• chr12-23354842-G-C
• chr12-23354842-G-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 0.712 in 151,990 control chromosomes in the GnomAD database, including 40,112 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 0.71 (40112 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 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: 0.712 AC: 108081 AN: 151872 Hom.: 40093 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.712 AC: 108142 AN: 151990 Hom.: 40112 Cov.: 31 AF XY: 0.717 AC XY: 53302 AN XY: 74300

African (AFR) AF: 0.488 AC: 20200 AN: 41418

American (AMR) AF: 0.719 AC: 10965 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2967 AN: 3468

East Asian (EAS) AF: 0.954 AC: 4926 AN: 5164

South Asian (SAS) AF: 0.871 AC: 4205 AN: 4830

European-Finnish (FIN) AF: 0.811 AC: 8585 AN: 10586

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53742 AN: 67956

Other (OTH) AF: 0.730 AC: 1535 AN: 2102

Alfa AF: 0.774 Hom.: 24575

Bravo AF: 0.697

Asia WGS AF: 0.853 AC: 2967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.26
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs7958592; hg19: chr12-23507776;