rs776472

Variant names:

• chr7-114712807-C-T
• rs776472

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.231 AC: 9585 AN: 41440

American (AMR) AF: 0.521 AC: 7955 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2153 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2643 AN: 5160

South Asian (SAS) AF: 0.610 AC: 2941 AN: 4820

European-Finnish (FIN) AF: 0.554 AC: 5854 AN: 10560

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39001 AN: 67946

Other (OTH) AF: 0.512 AC: 1082 AN: 2112

Alfa AF: 0.558 Hom.: 43676

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs776472; hg19: chr7-114352862;