rs1331567

Variant names:

• chr13-85321680-G-A
• rs1331567

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 0.347 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.307 AC: 12702 AN: 41388

American (AMR) AF: 0.332 AC: 5057 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1164 AN: 3464

East Asian (EAS) AF: 0.362 AC: 1874 AN: 5170

South Asian (SAS) AF: 0.271 AC: 1302 AN: 4806

European-Finnish (FIN) AF: 0.384 AC: 4042 AN: 10522

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25254 AN: 67824

Other (OTH) AF: 0.368 AC: 776 AN: 2106

Alfa AF: 0.362 Hom.: 1733

Bravo AF: 0.347

Asia WGS AF: 0.300 AC: 1040 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.16
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1331567; hg19: chr13-85895815;