rs754281

Positions:

• chr7-128932126-T-C

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 0.753 in 151,458 control chromosomes in the GnomAD database, including 43,874 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 0.75 (43874 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.00

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 (NFE) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.753 AC: 113945 AN: 151340 Hom.: 43867 Cov.: 27

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.753 AC: 113992 AN: 151458 Hom.: 43874 Cov.: 27 AF XY: 0.752 AC XY: 55673 AN XY: 73998

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.754

Alfa AF: 0.785 Hom.: 6749

Bravo AF: 0.730

Asia WGS AF: 0.716 AC: 2489 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	0.088
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754281; hg19: chr7-128572180;