chr6-159100096-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642586.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224478	ENST00000642586.1		n.412+5592C>T		intron	N/A
	ENSG00000285492	ENST00000642829.1		n.330-4197G>A		intron	N/A

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 v4.9

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;