rs17138705

Positions:

• chr11-79655278-C-T

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 0.141 in 152,010 control chromosomes in the GnomAD database, including 1,828 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 0.14 (1828 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.79655278C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21436 AN: 151892 Hom.: 1829 Cov.: 32

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.141 AC: 21465 AN: 152010 Hom.: 1828 Cov.: 32 AF XY: 0.145 AC XY: 10808 AN XY: 74286

Gnomad4 AFR AF: 0.0761

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.127

Alfa AF: 0.144 Hom.: 2217

Bravo AF: 0.143

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17138705; hg19: chr11-79366322;