rs7311964

Variant names:

• chr12-21260698-T-G
• rs7311964

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 0.231 in 151,982 control chromosomes in the GnomAD database, including 4,218 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 0.23 (4218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35013 AN: 151864 Hom.: 4209 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.231 AC: 35052 AN: 151982 Hom.: 4218 Cov.: 32 AF XY: 0.227 AC XY: 16865 AN XY: 74270

African (AFR) AF: 0.200 AC: 8312 AN: 41494

American (AMR) AF: 0.216 AC: 3297 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1508 AN: 5164

South Asian (SAS) AF: 0.356 AC: 1720 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1714 AN: 10566

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16432 AN: 67886

Other (OTH) AF: 0.234 AC: 495 AN: 2114

Alfa AF: 0.242 Hom.: 1917

Bravo AF: 0.234

Asia WGS AF: 0.338 AC: 1164 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.36
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7311964; hg19: chr12-21413632;