13-79056444-G-T

Variant names:

• chr13-79056444-G-T
• rs7988279

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 0.435 in 151,948 control chromosomes in the GnomAD database, including 14,700 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 0.44 (14700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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 (EAS) allele frequency at 95% confidence interval = 0.594 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: 0.435 AC: 66083 AN: 151830 Hom.: 14691 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.435 AC: 66102 AN: 151948 Hom.: 14700 Cov.: 32 AF XY: 0.437 AC XY: 32415 AN XY: 74258

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.422

Alfa AF: 0.455 Hom.: 7457

Bravo AF: 0.425

Asia WGS AF: 0.542 AC: 1879 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.083
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7988279; hg19: chr13-79630579;