rs17138705

Variant names:

• chr11-79655278-C-T
• rs17138705
• ENST00000789891.1:n.65-27863G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789891.1(ENSG00000302828):​n.65-27863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302828 ENST00000789891.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 1 publications found

Genes affected

ENSG00000302828 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302828	ENST00000789891.1	n.65-27863G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.0761 AC: 3158 AN: 41478

American (AMR) AF: 0.231 AC: 3527 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5160

South Asian (SAS) AF: 0.154 AC: 740 AN: 4802

European-Finnish (FIN) AF: 0.153 AC: 1615 AN: 10540

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10132 AN: 67980

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.143 Hom.: 2787

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17138705; hg19: chr11-79366322;