chr13-105453241-C-T

Variant names:

• chr13-105453241-C-T
• rs9519671

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 0.511 in 151,978 control chromosomes in the GnomAD database, including 20,082 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 0.51 (20082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 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: 0.511 AC: 77569 AN: 151860 Hom.: 20077 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.511 AC: 77614 AN: 151978 Hom.: 20082 Cov.: 32 AF XY: 0.508 AC XY: 37702 AN XY: 74282

African (AFR) AF: 0.448 AC: 18576 AN: 41440

American (AMR) AF: 0.527 AC: 8048 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1920 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1528 AN: 5156

South Asian (SAS) AF: 0.485 AC: 2334 AN: 4808

European-Finnish (FIN) AF: 0.525 AC: 5537 AN: 10548

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37901 AN: 67956

Other (OTH) AF: 0.530 AC: 1121 AN: 2114

Alfa AF: 0.516 Hom.: 6814

Bravo AF: 0.509

Asia WGS AF: 0.435 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.31
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9519671; hg19: chr13-106105590;