13-85321680-G-A

Position:

• chr13-85321680-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 0.347 in 151,710 control chromosomes in the GnomAD database, including 9,246 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 0.35 (9246 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52630 AN: 151594 Hom.: 9252 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.347 AC: 52645 AN: 151710 Hom.: 9246 Cov.: 31 AF XY: 0.345 AC XY: 25571 AN XY: 74112

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.368

Alfa AF: 0.363 Hom.: 1690

Bravo AF: 0.347

Asia WGS AF: 0.300 AC: 1040 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1331567; hg19: chr13-85895815;