7-50266267-T-G

Variant names:

• chr7-50266267-T-G
• rs4917014

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 0.269 in 152,252 control chromosomes in the GnomAD database, including 6,833 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 0.27 (6833 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906
• Publications: 149 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40881 AN: 152134 Hom.: 6829 Cov.: 33

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.269 AC: 40895 AN: 152252 Hom.: 6833 Cov.: 33 AF XY: 0.273 AC XY: 20344 AN XY: 74444

African (AFR) AF: 0.0849 AC: 3528 AN: 41574

American (AMR) AF: 0.480 AC: 7332 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1753 AN: 5184

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4826

European-Finnish (FIN) AF: 0.291 AC: 3090 AN: 10606

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22090 AN: 67984

Other (OTH) AF: 0.294 AC: 621 AN: 2110

Alfa AF: 0.312 Hom.: 37732

Bravo AF: 0.274

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4917014; hg19: chr7-50305863;