chr13-103965585-T-C

Variant names:

• chr13-103965585-T-C
• rs17413237

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 0.0607 in 152,240 control chromosomes in the GnomAD database, including 351 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 0.061 (351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9230 AN: 152122 Hom.: 349 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0607 AC: 9247 AN: 152240 Hom.: 351 Cov.: 32 AF XY: 0.0590 AC XY: 4395 AN XY: 74434

African (AFR) AF: 0.0994 AC: 4129 AN: 41526

American (AMR) AF: 0.0355 AC: 543 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0269 AC: 130 AN: 4832

European-Finnish (FIN) AF: 0.0342 AC: 363 AN: 10610

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0570 AC: 3877 AN: 67996

Other (OTH) AF: 0.0539 AC: 114 AN: 2116

Alfa AF: 0.0588 Hom.: 47

Bravo AF: 0.0625

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs17413237; hg19: chr13-104617935;