13-105444546-A-T

Variant names:

• chr13-105444546-A-T
• rs7981258

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 0.645 in 152,060 control chromosomes in the GnomAD database, including 32,241 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 0.64 (32241 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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: 0.645 AC: 97972 AN: 151942 Hom.: 32225 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.645 AC: 98029 AN: 152060 Hom.: 32241 Cov.: 31 AF XY: 0.647 AC XY: 48073 AN XY: 74328

African (AFR) AF: 0.512 AC: 21235 AN: 41444

American (AMR) AF: 0.727 AC: 11120 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4490 AN: 5168

South Asian (SAS) AF: 0.656 AC: 3163 AN: 4818

European-Finnish (FIN) AF: 0.725 AC: 7671 AN: 10578

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46136 AN: 67978

Other (OTH) AF: 0.650 AC: 1371 AN: 2110

Alfa AF: 0.650 Hom.: 4039

Bravo AF: 0.643

Asia WGS AF: 0.750 AC: 2609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.59
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs7981258; hg19: chr13-106096895;