rs17135859

Variant names:

• chr5-113660957-T-C
• rs17135859
• ENST00000810862.1:n.390+7355T>C

Variant summary

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

The ENST00000810862.1(ENSG00000305424):​n.390+7355T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,220 control chromosomes in the GnomAD database, including 2,249 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 0.16 (2249 hom., cov: 32)
• Consequence: ENSG00000305424 ENST00000810862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 6 publications found

Genes affected

ENSG00000305424 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986441	XR_001742841.1	n.59+27593T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305424	ENST00000810862.1	n.390+7355T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25093 AN: 152100 Hom.: 2245 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.165 AC: 25115 AN: 152220 Hom.: 2249 Cov.: 32 AF XY: 0.161 AC XY: 11962 AN XY: 74420

African (AFR) AF: 0.217 AC: 8996 AN: 41540

American (AMR) AF: 0.160 AC: 2451 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5188

South Asian (SAS) AF: 0.111 AC: 537 AN: 4820

European-Finnish (FIN) AF: 0.134 AC: 1418 AN: 10598

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10824 AN: 68004

Other (OTH) AF: 0.143 AC: 301 AN: 2110

Alfa AF: 0.157 Hom.: 8584

Bravo AF: 0.169

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs17135859; hg19: chr5-112996654; COSMIC: COSV50462836;