13-70373320-A-G

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 0.316 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.312

Alfa AF: 0.342 Hom.: 5357

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

Splicing

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

Publications

LitVar

Other links and lift over

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