rs17642174

Variant names:

• chr4-28549715-A-T
• rs17642174
• ENST00000509416.1:n.403-28201A>T

Variant summary

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

The ENST00000509416.1(ENSG00000250064):​n.403-28201A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 151,896 control chromosomes in the GnomAD database, including 1,373 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 0.12 (1373 hom., cov: 32)
• Consequence: ENSG00000250064 ENST00000509416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 1 publications found

Genes affected

ENSG00000250064 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374557	NR_188396.1	n.348-28201A>T		intron_variant	Intron 3 of 4
LOC105374557	NR_188397.1	n.348-50332A>T		intron_variant	Intron 3 of 3
LOC105374557	NR_188399.1	n.301-50332A>T		intron_variant	Intron 2 of 2
LOC105374558	XR_925528.3	n.332-26559T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250064	ENST00000509416.1	n.403-28201A>T		intron_variant	Intron 2 of 3	3
ENSG00000250064	ENST00000729962.1	n.219-28201A>T		intron_variant	Intron 2 of 3
ENSG00000250064	ENST00000729963.1	n.211-2660A>T		intron_variant	Intron 2 of 2
ENSG00000250064	ENST00000729966.1	n.92+897A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18743 AN: 151778 Hom.: 1375 Cov.: 32

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.123 AC: 18736 AN: 151896 Hom.: 1373 Cov.: 32 AF XY: 0.126 AC XY: 9365 AN XY: 74252

African (AFR) AF: 0.0536 AC: 2225 AN: 41490

American (AMR) AF: 0.113 AC: 1722 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3462

East Asian (EAS) AF: 0.145 AC: 748 AN: 5148

South Asian (SAS) AF: 0.266 AC: 1278 AN: 4810

European-Finnish (FIN) AF: 0.128 AC: 1350 AN: 10578

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10204 AN: 67874

Other (OTH) AF: 0.129 AC: 272 AN: 2108

Alfa AF: 0.131 Hom.: 183

Bravo AF: 0.118

Asia WGS AF: 0.183 AC: 635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.73
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs17642174; hg19: chr4-28551337;