rs17642091

Variant names:

• chr17-78332756-G-A
• rs17642091
• ENST00000586321.1:n.61-11209G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-78332756-G-A
• chr17-78332756-G-T

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-11209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,122 control chromosomes in the GnomAD database, including 2,015 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 (2015 hom., cov: 31)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 5 publications found

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586321.1. 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
	LOC105371912	NR_188632.1		n.74-11209G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267737	ENST00000586321.1	TSL:3	n.61-11209G>A		intron	N/A
	ENSG00000267737	ENST00000823930.1		n.39-11209G>A		intron	N/A
	ENSG00000267737	ENST00000823931.1		n.72-11209G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20718 AN: 152004 Hom.: 2017 Cov.: 31

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.136 AC: 20720 AN: 152122 Hom.: 2015 Cov.: 31 AF XY: 0.138 AC XY: 10226 AN XY: 74326

African (AFR) AF: 0.0340 AC: 1412 AN: 41534

American (AMR) AF: 0.100 AC: 1528 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5178

South Asian (SAS) AF: 0.0535 AC: 258 AN: 4820

European-Finnish (FIN) AF: 0.289 AC: 3054 AN: 10560

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13740 AN: 67978

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.176 Hom.: 2490

Bravo AF: 0.117

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.82
PhyloP100		-0.23

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: rs17642091;

hg19: chr17-76328837;