17-21268977-G-C

Variant names:

• chr17-21268977-G-C
• rs11652094

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 0.727 in 152,116 control chromosomes in the GnomAD database, including 40,903 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 0.73 (40903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.849 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: 0.727 AC: 110517 AN: 151996 Hom.: 40872 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.727 AC: 110609 AN: 152116 Hom.: 40903 Cov.: 33 AF XY: 0.726 AC XY: 53974 AN XY: 74332

African (AFR) AF: 0.856 AC: 35546 AN: 41522

American (AMR) AF: 0.589 AC: 9007 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2246 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2891 AN: 5164

South Asian (SAS) AF: 0.718 AC: 3465 AN: 4828

European-Finnish (FIN) AF: 0.738 AC: 7792 AN: 10558

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47212 AN: 67974

Other (OTH) AF: 0.706 AC: 1491 AN: 2112

Alfa AF: 0.636 Hom.: 1894

Bravo AF: 0.716

Asia WGS AF: 0.688 AC: 2395 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	0.83
DANN	Benign	0.52
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11652094; hg19: chr17-21172289;