rs2451241

Variant names:

• chr6-159100096-C-T
• rs2451241
• ENST00000642586.1:n.412+5592C>T

Variant summary

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

The ENST00000642586.1(ENSG00000224478):​n.412+5592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,814 control chromosomes in the GnomAD database, including 11,289 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 0.38 (11289 hom., cov: 30)
• Consequence: ENSG00000224478 ENST00000642586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 3 publications found

Genes affected

ENSG00000224478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267968	XM_047419645.1	c.153-4197G>A		intron_variant	Intron 2 of 4		XP_047275601.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224478	ENST00000642586.1	n.412+5592C>T		intron_variant	Intron 1 of 4
ENSG00000285492	ENST00000642829.1	n.330-4197G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57460 AN: 151696 Hom.: 11284 Cov.: 30

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.379 AC: 57470 AN: 151814 Hom.: 11289 Cov.: 30 AF XY: 0.378 AC XY: 28021 AN XY: 74174

African (AFR) AF: 0.312 AC: 12889 AN: 41362

American (AMR) AF: 0.321 AC: 4895 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1236 AN: 3466

East Asian (EAS) AF: 0.237 AC: 1223 AN: 5160

South Asian (SAS) AF: 0.436 AC: 2103 AN: 4824

European-Finnish (FIN) AF: 0.439 AC: 4608 AN: 10490

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29340 AN: 67928

Other (OTH) AF: 0.388 AC: 818 AN: 2108

Alfa AF: 0.409 Hom.: 41512

Bravo AF: 0.359

Asia WGS AF: 0.393 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.039
DANN	Benign	0.57
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2451241; hg19: chr6-159521128; COSMIC: COSV55964990;