chr17-13225826-C-T

Variant names:

• chr17-13225826-C-T
• rs10521211

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 0.308 in 152,086 control chromosomes in the GnomAD database, including 8,256 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 0.31 (8256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 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: 0.308 AC: 46785 AN: 151968 Hom.: 8253 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.308 AC: 46781 AN: 152086 Hom.: 8256 Cov.: 32 AF XY: 0.303 AC XY: 22506 AN XY: 74340

African (AFR) AF: 0.137 AC: 5692 AN: 41506

American (AMR) AF: 0.283 AC: 4324 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3468

East Asian (EAS) AF: 0.188 AC: 970 AN: 5166

South Asian (SAS) AF: 0.336 AC: 1622 AN: 4828

European-Finnish (FIN) AF: 0.341 AC: 3601 AN: 10560

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27969 AN: 67964

Other (OTH) AF: 0.345 AC: 729 AN: 2112

Alfa AF: 0.368 Hom.: 5440

Bravo AF: 0.295

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10521211; hg19: chr17-13129143; COSMIC: COSV60074044;