13-71304492-A-T

Variant names:

• chr13-71304492-A-T
• rs2325367

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 0.952 in 152,196 control chromosomes in the GnomAD database, including 69,170 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 0.95 (69170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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: 0.952 AC: 144717 AN: 152078 Hom.: 69126 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.963

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

GnomAD4 genome AF: 0.952 AC: 144819 AN: 152196 Hom.: 69170 Cov.: 32 AF XY: 0.953 AC XY: 70916 AN XY: 74436

African (AFR) AF: 0.852 AC: 35384 AN: 41520

American (AMR) AF: 0.959 AC: 14648 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3402 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5142 AN: 5170

South Asian (SAS) AF: 0.982 AC: 4739 AN: 4826

European-Finnish (FIN) AF: 0.999 AC: 10586 AN: 10592

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67680 AN: 68018

Other (OTH) AF: 0.964 AC: 2035 AN: 2112

Alfa AF: 0.970 Hom.: 8908

Bravo AF: 0.944

Asia WGS AF: 0.975 AC: 3374 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.46
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2325367; hg19: chr13-71878624;