7-150940775-C-T

Variant names:

• chr7-150940775-C-T
• rs4725982

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.265 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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.271

Alfa AF: 0.234 Hom.: 10187

Bravo AF: 0.271

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4725982; hg19: chr7-150637863;