rs78043697

Variant names:

• chr13-61892906-T-C
• rs78043697

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0465 AC: 1932 AN: 41550

American (AMR) AF: 0.0413 AC: 632 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3472

East Asian (EAS) AF: 0.0543 AC: 281 AN: 5176

South Asian (SAS) AF: 0.0693 AC: 334 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1137 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5202 AN: 68008

Other (OTH) AF: 0.0530 AC: 112 AN: 2112

Alfa AF: 0.0806 Hom.: 60

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
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs78043697; hg19: chr13-62467039;