rs3132451

Variant names:

• chr6-31614248-G-C
• rs3132451
• ENST00000782490.1:n.218-2542C>G

Variant summary

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

The ENST00000782490.1(ENSG00000289375):​n.218-2542C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,214 control chromosomes in the GnomAD database, including 2,562 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 (2562 hom., cov: 32)
• Consequence: ENSG00000289375 ENST00000782490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 49 publications found

Genes affected

ENSG00000289375 (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 = 0.192 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
ENSG00000289375	ENST00000782490.1	n.218-2542C>G		intron_variant	Intron 1 of 1
ENSG00000289375	ENST00000782491.1	n.306+2149C>G		intron_variant	Intron 2 of 2
ENSG00000289375	ENST00000782492.1	n.153-2538C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26675 AN: 152096 Hom.: 2562 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.175 AC: 26674 AN: 152214 Hom.: 2562 Cov.: 32 AF XY: 0.170 AC XY: 12658 AN XY: 74418

African (AFR) AF: 0.195 AC: 8085 AN: 41522

American (AMR) AF: 0.104 AC: 1584 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3472

East Asian (EAS) AF: 0.0792 AC: 411 AN: 5188

South Asian (SAS) AF: 0.125 AC: 603 AN: 4830

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10592

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13276 AN: 68002

Other (OTH) AF: 0.151 AC: 318 AN: 2108

Alfa AF: 0.194 Hom.: 1720

Bravo AF: 0.173

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs3132451; hg19: chr6-31582025;