rs7754768

Variant names:

• chr6-32452402-C-T
• rs7754768

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;