rs7311660

Positions:

• chr12-74660813-A-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 0.467 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;