chr17-82710148-T-C

Variant names:

• chr17-82710148-T-C
• rs11869249

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 0.213 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.213 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

African (AFR) AF: 0.224 AC: 9317 AN: 41514

American (AMR) AF: 0.252 AC: 3848 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3468

East Asian (EAS) AF: 0.0614 AC: 318 AN: 5178

South Asian (SAS) AF: 0.174 AC: 842 AN: 4828

European-Finnish (FIN) AF: 0.193 AC: 2048 AN: 10592

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14688 AN: 67972

Other (OTH) AF: 0.223 AC: 469 AN: 2106

Alfa AF: 0.221 Hom.: 5605

Bravo AF: 0.218

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.19
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs11869249; hg19: chr17-80668024;