rs17407594

Variant names:

• chr1-65704679-G-A
• rs17407594
• ENST00000646875.2:n.347+373G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-65704679-G-A
• chr1-65704679-G-C
• chr1-65704679-G-T

Variant summary

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

The ENST00000646875.2(ENSG00000285079):​n.347+373G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,142 control chromosomes in the GnomAD database, including 1,589 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 0.13 (1589 hom., cov: 32)
• Consequence: ENSG00000285079 ENST00000646875.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.735
• Publications: 7 publications found

Genes affected

ENSG00000285079 (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 (AMR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646875.2. 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
	ENSG00000285079	ENST00000646875.2		n.347+373G>A		intron	N/A
	ENSG00000285079	ENST00000760543.1		n.364+373G>A		intron	N/A
	ENSG00000285079	ENST00000760544.1		n.290+373G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19888 AN: 152026 Hom.: 1586 Cov.: 32

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.131 AC: 19898 AN: 152142 Hom.: 1589 Cov.: 32 AF XY: 0.130 AC XY: 9680 AN XY: 74370

African (AFR) AF: 0.0532 AC: 2209 AN: 41518

American (AMR) AF: 0.186 AC: 2852 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3468

East Asian (EAS) AF: 0.0891 AC: 462 AN: 5186

South Asian (SAS) AF: 0.126 AC: 608 AN: 4810

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10570

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11241 AN: 67982

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.154 Hom.: 5625

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.33
PhyloP100		0.73

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: rs17407594;

hg19: chr1-66170362;