rs7755852

Positions:

• chr6-31310211-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 0.492 in 146,918 control chromosomes in the GnomAD database, including 21,266 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 0.49 (21266 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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: 0.492 AC: 72294 AN: 146806 Hom.: 21255 Cov.: 29

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.492 AC: 72322 AN: 146918 Hom.: 21266 Cov.: 29 AF XY: 0.487 AC XY: 34784 AN XY: 71436

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.464

Alfa AF: 0.549 Hom.: 16059

Asia WGS AF: 0.445 AC: 1441 AN: 3240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7755852; hg19: chr6-31277988;