rs13207034

Variant names:

• chr6-92487582-G-A
• rs13207034

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 0.0728 in 152,188 control chromosomes in the GnomAD database, including 733 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 0.073 (733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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: 0.0727 AC: 11056 AN: 152070 Hom.: 725 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0811

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

GnomAD4 genome AF: 0.0728 AC: 11085 AN: 152188 Hom.: 733 Cov.: 32 AF XY: 0.0751 AC XY: 5586 AN XY: 74388

African (AFR) AF: 0.0156 AC: 648 AN: 41540

American (AMR) AF: 0.187 AC: 2856 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1467 AN: 5140

South Asian (SAS) AF: 0.141 AC: 680 AN: 4824

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10618

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4805 AN: 68000

Other (OTH) AF: 0.0878 AC: 185 AN: 2106

Alfa AF: 0.0616 Hom.: 210

Bravo AF: 0.0839

Asia WGS AF: 0.192 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.17
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs13207034; hg19: chr6-93197300;