rs178733

Variant names:

• chr7-128135297-T-A
• rs178733

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 0.482 in 151,996 control chromosomes in the GnomAD database, including 18,857 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 0.48 (18857 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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: 0.482 AC: 73168 AN: 151876 Hom.: 18825 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.482 AC: 73258 AN: 151996 Hom.: 18857 Cov.: 31 AF XY: 0.474 AC XY: 35233 AN XY: 74304

African (AFR) AF: 0.663 AC: 27476 AN: 41420

American (AMR) AF: 0.474 AC: 7238 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1602 AN: 3470

East Asian (EAS) AF: 0.161 AC: 832 AN: 5156

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4822

European-Finnish (FIN) AF: 0.378 AC: 3997 AN: 10586

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28972 AN: 67960

Other (OTH) AF: 0.445 AC: 940 AN: 2110

Alfa AF: 0.461 Hom.: 2096

Bravo AF: 0.500

Asia WGS AF: 0.287 AC: 1000 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.58
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs178733; hg19: chr7-127775349;