13-70373320-A-G

Variant names:

• chr13-70373320-A-G
• rs1155635

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 0.316 in 152,056 control chromosomes in the GnomAD database, including 8,055 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 0.32 (8055 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.316 AC: 47981 AN: 151938 Hom.: 8055 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.316 AC: 47983 AN: 152056 Hom.: 8055 Cov.: 33 AF XY: 0.310 AC XY: 23013 AN XY: 74302

African (AFR) AF: 0.206 AC: 8554 AN: 41512

American (AMR) AF: 0.353 AC: 5395 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1105 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2033 AN: 5158

South Asian (SAS) AF: 0.304 AC: 1465 AN: 4826

European-Finnish (FIN) AF: 0.301 AC: 3177 AN: 10572

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25267 AN: 67944

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.343 Hom.: 6741

Bravo AF: 0.316

Asia WGS AF: 0.344 AC: 1196 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1155635; hg19: chr13-70947452; COSMIC: COSV69362186;