rs7754768

Positions:

• chr6-32452402-C-T

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 0.567 in 151,818 control chromosomes in the GnomAD database, including 24,808 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 0.57 (24808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.635 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: 0.567 AC: 85956 AN: 151700 Hom.: 24796 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.567 AC: 86008 AN: 151818 Hom.: 24808 Cov.: 32 AF XY: 0.566 AC XY: 42025 AN XY: 74196

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.604

Alfa AF: 0.595 Hom.: 32017

Bravo AF: 0.576

Asia WGS AF: 0.542 AC: 1888 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	2.6
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7754768; hg19: chr6-32420179; COSMIC: COSV51803812;