rs17542348

Variant names:

• chr7-11291017-C-T
• rs17542348
• ENST00000421121.5:n.113+37792C>T

Variant summary

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

The ENST00000421121.5(ENSG00000230333):​n.113+37792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 151,752 control chromosomes in the GnomAD database, including 3,356 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 0.18 (3356 hom., cov: 32)
• Consequence: ENSG00000230333 ENST00000421121.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 2 publications found

Genes affected

ENSG00000230333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230333	ENST00000421121.5	n.113+37792C>T		intron_variant	Intron 1 of 2	1
ENSG00000230333	ENST00000428533.5	n.139-88270C>T		intron_variant	Intron 1 of 2	5
ENSG00000230333	ENST00000428967.5	n.497+42642C>T		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27634 AN: 151634 Hom.: 3355 Cov.: 32

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.182 AC: 27631 AN: 151752 Hom.: 3356 Cov.: 32 AF XY: 0.184 AC XY: 13643 AN XY: 74148

African (AFR) AF: 0.0441 AC: 1828 AN: 41446

American (AMR) AF: 0.140 AC: 2124 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3464

East Asian (EAS) AF: 0.0146 AC: 75 AN: 5128

South Asian (SAS) AF: 0.134 AC: 645 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3558 AN: 10542

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17650 AN: 67828

Other (OTH) AF: 0.196 AC: 411 AN: 2102

Alfa AF: 0.213 Hom.: 717

Bravo AF: 0.162

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.73
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs17542348; hg19: chr7-11330644;