rs849376

Variant names:

• chr7-106853873-C-T
• rs849376

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 0.126 in 152,196 control chromosomes in the GnomAD database, including 1,591 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 0.13 (1591 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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: 0.126 AC: 19201 AN: 152078 Hom.: 1586 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.126 AC: 19228 AN: 152196 Hom.: 1591 Cov.: 33 AF XY: 0.129 AC XY: 9571 AN XY: 74410

African (AFR) AF: 0.167 AC: 6935 AN: 41500

American (AMR) AF: 0.198 AC: 3024 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1889 AN: 5168

South Asian (SAS) AF: 0.0893 AC: 431 AN: 4826

European-Finnish (FIN) AF: 0.0839 AC: 889 AN: 10598

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5321 AN: 68022

Other (OTH) AF: 0.120 AC: 253 AN: 2112

Alfa AF: 0.0958 Hom.: 3911

Bravo AF: 0.138

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.073
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs849376; hg19: chr7-106494318;