rs17238902

Variant names:

• chr10-65889620-G-A
• rs17238902
• ENST00000811922.1:n.186+1685C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-65889620-G-A
• chr10-65889620-G-T

Variant summary

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

The ENST00000811922.1(ENSG00000305605):​n.186+1685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,086 control chromosomes in the GnomAD database, including 1,090 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 0.11 (1090 hom., cov: 32)
• Consequence: ENSG00000305605 ENST00000811922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

ENSG00000305605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378339	XR_001747476.2	n.200+1685C>T		intron_variant	Intron 1 of 6
LOC105378339	XR_946023.4	n.200+1685C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305605	ENST00000811922.1	n.186+1685C>T		intron_variant	Intron 1 of 1
ENSG00000305605	ENST00000811923.1	n.176+1685C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16795 AN: 151966 Hom.: 1090 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.110 AC: 16797 AN: 152086 Hom.: 1090 Cov.: 32 AF XY: 0.111 AC XY: 8215 AN XY: 74330

African (AFR) AF: 0.0697 AC: 2889 AN: 41470

American (AMR) AF: 0.155 AC: 2375 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3472

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5188

South Asian (SAS) AF: 0.136 AC: 658 AN: 4824

European-Finnish (FIN) AF: 0.105 AC: 1103 AN: 10554

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8589 AN: 67982

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.124 Hom.: 1729

Bravo AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.50
PhyloP100		0.088

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17238902; hg19: chr10-67649378;