rs1331567

Variant names:

• chr13-85321680-G-A
• rs1331567

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;