rs776472

Positions:

• chr7-114712807-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 0.474 in 151,972 control chromosomes in the GnomAD database, including 18,905 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 (18905 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.592 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: 0.474 AC: 72043 AN: 151854 Hom.: 18904 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.474 AC: 72080 AN: 151972 Hom.: 18905 Cov.: 31 AF XY: 0.476 AC XY: 35350 AN XY: 74262

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.512

Alfa AF: 0.568 Hom.: 36263

Bravo AF: 0.462

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs776472; hg19: chr7-114352862;