7-128951310-A-T

Variant names:

• chr7-128951310-A-T
• rs13242262

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 0.579 in 152,084 control chromosomes in the GnomAD database, including 25,764 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 0.58 (25764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 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: 0.579 AC: 87977 AN: 151966 Hom.: 25753 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.579 AC: 88028 AN: 152084 Hom.: 25764 Cov.: 32 AF XY: 0.577 AC XY: 42882 AN XY: 74344

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.597

Alfa AF: 0.587 Hom.: 3166

Bravo AF: 0.572

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13242262; hg19: chr7-128591364;