rs7311660

Variant names:

• chr12-74660813-A-G
• rs7311660

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 0.467 in 151,978 control chromosomes in the GnomAD database, including 18,823 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 0.47 (18823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.467 AC: 70851 AN: 151860 Hom.: 18796 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.467 AC: 70924 AN: 151978 Hom.: 18823 Cov.: 32 AF XY: 0.465 AC XY: 34505 AN XY: 74264

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.439

Alfa AF: 0.381 Hom.: 4302

Bravo AF: 0.479

Asia WGS AF: 0.398 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.017
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7311660; hg19: chr12-75054593;