chr13-68440680-G-A

Position:

• chr13-68440680-G-A

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 0.112 in 149,272 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.176 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: 0.112 AC: 16689 AN: 149188 Hom.: 1039 Cov.: 31

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.112 AC: 16708 AN: 149272 Hom.: 1040 Cov.: 31 AF XY: 0.114 AC XY: 8303 AN XY: 72678

Gnomad4 AFR AF: 0.0732

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0776

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.133

Alfa AF: 0.117 Hom.: 540

Bravo AF: 0.118

Asia WGS AF: 0.176 AC: 607 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966715; hg19: chr13-69014812;