rs7311964

chr12-21260698-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.234

Alfa AF: 0.243 Hom.: 1747

Bravo AF: 0.234

Asia WGS AF: 0.338 AC: 1164 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.4
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7311964; hg19: chr12-21413632;