rs78043697

chr13-61892906-T-C

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 0.0652 in 152,240 control chromosomes in the GnomAD database, including 337 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 0.065 (337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9922 AN: 152122 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.0545

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0652 AC: 9928 AN: 152240 Hom.: 337 Cov.: 32 AF XY: 0.0667 AC XY: 4964 AN XY: 74436

Gnomad4 AFR AF: 0.0465

Gnomad4 AMR AF: 0.0413

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.0543

Gnomad4 SAS AF: 0.0693

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0822 Hom.: 58

Bravo AF: 0.0571

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	13
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78043697; hg19: chr13-62467039;