ENST00000637627.1:n.332+9484C>T

Variant names:

• chr17-71849137-G-A
• rs12451750
• ENST00000637627.1:n.332+9484C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637627.1(ENSG00000283517):​n.332+9484C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,138 control chromosomes in the GnomAD database, including 1,657 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 (1657 hom., cov: 32)
• Consequence: ENSG00000283517 ENST00000637627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

Genes affected

ENSG00000283517 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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
ENSG00000283517	ENST00000637627.1	n.332+9484C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19177 AN: 152022 Hom.: 1658 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.126 AC: 19180 AN: 152138 Hom.: 1657 Cov.: 32 AF XY: 0.128 AC XY: 9539 AN XY: 74388

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.0927

Gnomad4 FIN AF: 0.0889

Gnomad4 NFE AF: 0.0682

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0859 Hom.: 328

Bravo AF: 0.140

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12451750; hg19: chr17-69845278;