chr13-75984017-T-C

Variant names:

• chr13-75984017-T-C
• rs9544105

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 0.209 in 152,204 control chromosomes in the GnomAD database, including 4,216 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 0.21 (4216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 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: 0.209 AC: 31754 AN: 152086 Hom.: 4214 Cov.: 32

Gnomad AFR AF: 0.0754

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.209 AC: 31761 AN: 152204 Hom.: 4216 Cov.: 32 AF XY: 0.212 AC XY: 15769 AN XY: 74420

African (AFR) AF: 0.0753 AC: 3131 AN: 41562

American (AMR) AF: 0.145 AC: 2217 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3472

East Asian (EAS) AF: 0.111 AC: 578 AN: 5188

South Asian (SAS) AF: 0.182 AC: 879 AN: 4822

European-Finnish (FIN) AF: 0.395 AC: 4174 AN: 10574

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19354 AN: 67970

Other (OTH) AF: 0.191 AC: 403 AN: 2114

Alfa AF: 0.248 Hom.: 8590

Bravo AF: 0.183

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs9544105; hg19: chr13-76558153;