7-128239315-C-T

Position:

• chr7-128239315-C-T

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 0.374 in 152,070 control chromosomes in the GnomAD database, including 12,796 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 0.37 (12796 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56777 AN: 151952 Hom.: 12792 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.374 AC: 56800 AN: 152070 Hom.: 12796 Cov.: 31 AF XY: 0.384 AC XY: 28536 AN XY: 74334

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.380

Alfa AF: 0.272 Hom.: 781

Bravo AF: 0.354

Asia WGS AF: 0.626 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12536535; hg19: chr7-127879368;