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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810862.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000305424	ENST00000810862.1		n.390+7355T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17135859;

hg19: chr5-112996654;

COSMIC: COSV50462836;