7-42279457-C-T

Variant names:

• chr7-42279457-C-T
• rs886827

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 0.639 in 151,898 control chromosomes in the GnomAD database, including 31,676 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 0.64 (31676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 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: 0.639 AC: 97022 AN: 151780 Hom.: 31649 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.639 AC: 97096 AN: 151898 Hom.: 31676 Cov.: 32 AF XY: 0.643 AC XY: 47767 AN XY: 74266

African (AFR) AF: 0.521 AC: 21564 AN: 41388

American (AMR) AF: 0.613 AC: 9357 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2318 AN: 3466

East Asian (EAS) AF: 0.687 AC: 3546 AN: 5164

South Asian (SAS) AF: 0.622 AC: 2997 AN: 4816

European-Finnish (FIN) AF: 0.771 AC: 8128 AN: 10542

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46949 AN: 67946

Other (OTH) AF: 0.639 AC: 1345 AN: 2104

Alfa AF: 0.667 Hom.: 43137

Bravo AF: 0.620

Asia WGS AF: 0.643 AC: 2229 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.60
DANN	Benign	0.51
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs886827; hg19: chr7-42319056;