chr13-91080516-A-T

Variant names:

• chr13-91080516-A-T
• rs61970269

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 0.363 in 150,044 control chromosomes in the GnomAD database, including 10,149 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 0.36 (10149 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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: 0.363 AC: 54434 AN: 149930 Hom.: 10122 Cov.: 25

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.363 AC: 54512 AN: 150044 Hom.: 10149 Cov.: 25 AF XY: 0.367 AC XY: 26862 AN XY: 73198

African (AFR) AF: 0.366 AC: 14902 AN: 40662

American (AMR) AF: 0.416 AC: 6265 AN: 15066

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 921 AN: 3454

East Asian (EAS) AF: 0.431 AC: 2172 AN: 5034

South Asian (SAS) AF: 0.346 AC: 1634 AN: 4720

European-Finnish (FIN) AF: 0.394 AC: 4031 AN: 10240

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.349 AC: 23596 AN: 67576

Other (OTH) AF: 0.323 AC: 675 AN: 2090

Alfa AF: 0.367 Hom.: 1341

Bravo AF: 0.367

Asia WGS AF: 0.389 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs61970269; hg19: chr13-91732770;