7-150940775-C-T

Variant names:

• chr7-150940775-C-T
• rs4725982

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 0.265 in 152,154 control chromosomes in the GnomAD database, including 5,970 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 (5970 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.265 AC: 40337 AN: 152036 Hom.: 5950 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.265 AC: 40388 AN: 152154 Hom.: 5970 Cov.: 33 AF XY: 0.273 AC XY: 20329 AN XY: 74354

African (AFR) AF: 0.259 AC: 10753 AN: 41504

American (AMR) AF: 0.330 AC: 5052 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3472

East Asian (EAS) AF: 0.622 AC: 3223 AN: 5178

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4818

European-Finnish (FIN) AF: 0.306 AC: 3233 AN: 10582

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14496 AN: 67992

Other (OTH) AF: 0.271 AC: 571 AN: 2110

Alfa AF: 0.238 Hom.: 20917

Bravo AF: 0.271

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.036
DANN	Benign	0.69
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4725982; hg19: chr7-150637863;