chr13-70190056-A-G

Variant names:

• chr13-70190056-A-G
• rs9542207

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 0.0887 in 151,674 control chromosomes in the GnomAD database, including 854 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 0.089 (854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 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: 0.0887 AC: 13450 AN: 151556 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.0551

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0887 AC: 13454 AN: 151674 Hom.: 854 Cov.: 32 AF XY: 0.0853 AC XY: 6323 AN XY: 74138

African (AFR) AF: 0.0321 AC: 1332 AN: 41472

American (AMR) AF: 0.0764 AC: 1158 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0900 AC: 311 AN: 3456

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5158

South Asian (SAS) AF: 0.0488 AC: 235 AN: 4816

European-Finnish (FIN) AF: 0.0983 AC: 1042 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9098 AN: 67696

Other (OTH) AF: 0.101 AC: 213 AN: 2106

Alfa AF: 0.101 Hom.: 153

Bravo AF: 0.0834

Asia WGS AF: 0.0210 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.40
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs9542207; hg19: chr13-70764188; COSMIC: COSV69361895;