7-128920707-G-T

Variant names:

• chr7-128920707-G-T
• rs960633

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 0.234 in 152,050 control chromosomes in the GnomAD database, including 4,766 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 0.23 (4766 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.234 AC: 35523 AN: 151932 Hom.: 4765 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.234 AC: 35526 AN: 152050 Hom.: 4766 Cov.: 32 AF XY: 0.233 AC XY: 17328 AN XY: 74318

African (AFR) AF: 0.106 AC: 4417 AN: 41474

American (AMR) AF: 0.287 AC: 4389 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3466

East Asian (EAS) AF: 0.108 AC: 561 AN: 5176

South Asian (SAS) AF: 0.191 AC: 923 AN: 4822

European-Finnish (FIN) AF: 0.287 AC: 3027 AN: 10544

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19886 AN: 67972

Other (OTH) AF: 0.267 AC: 563 AN: 2110

Alfa AF: 0.271 Hom.: 10996

Bravo AF: 0.233

Asia WGS AF: 0.173 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs960633; hg19: chr7-128560761;