chr13-39997916-G-A

Position:

• chr13-39997916-G-A

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 0.299 in 151,980 control chromosomes in the GnomAD database, including 7,533 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 0.30 (7533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.382 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: 0.300 AC: 45487 AN: 151862 Hom.: 7531 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.299 AC: 45500 AN: 151980 Hom.: 7533 Cov.: 32 AF XY: 0.297 AC XY: 22091 AN XY: 74286

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.292

Alfa AF: 0.349 Hom.: 5026

Bravo AF: 0.299

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7339164; hg19: chr13-40572053; COSMIC: COSV69954097;