chr17-82710148-T-C

Variant names:

• chr17-82710148-T-C
• rs11869249

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.213 in 152,158 control chromosomes in the GnomAD database, including 3,507 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 (3507 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 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: 0.213 AC: 32402 AN: 152040 Hom.: 3503 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.213 AC: 32423 AN: 152158 Hom.: 3507 Cov.: 33 AF XY: 0.211 AC XY: 15689 AN XY: 74394

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0614

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.223

Alfa AF: 0.219 Hom.: 4343

Bravo AF: 0.218

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11869249; hg19: chr17-80668024;