7-131603090-C-T

Position:

• chr7-131603090-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 0.373 in 151,914 control chromosomes in the GnomAD database, including 12,050 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 (12050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 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: 56701 AN: 151796 Hom.: 12053 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.373 AC: 56708 AN: 151914 Hom.: 12050 Cov.: 32 AF XY: 0.376 AC XY: 27943 AN XY: 74230

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.380

Alfa AF: 0.434 Hom.: 13933

Bravo AF: 0.349

Asia WGS AF: 0.421 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862083; hg19: chr7-131287849;