rs7319068

Variant names:

• chr13-23107522-G-T
• rs7319068

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 0.746 in 152,160 control chromosomes in the GnomAD database, including 42,889 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 (42889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 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: 0.746 AC: 113479 AN: 152042 Hom.: 42847 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.746 AC: 113570 AN: 152160 Hom.: 42889 Cov.: 32 AF XY: 0.740 AC XY: 55018 AN XY: 74378

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.728

Alfa AF: 0.728 Hom.: 40037

Bravo AF: 0.745

Asia WGS AF: 0.774 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.068
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7319068; hg19: chr13-23681661;