chr6-38673578-C-T

Variant names:

• chr6-38673578-C-T
• rs6458065
• ENST00000755274.1:n.480+18911C>T

Variant summary

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

The ENST00000755274.1(ENSG00000298390):​n.480+18911C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,922 control chromosomes in the GnomAD database, including 22,237 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 0.54 (22237 hom., cov: 31)
• Consequence: ENSG00000298390 ENST00000755274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 8 publications found

Genes affected

ENSG00000298390 (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 (AFR) allele frequency at 95% confidence interval = 0.558 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
ENSG00000298390	ENST00000755274.1	n.480+18911C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81627 AN: 151804 Hom.: 22222 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.538 AC: 81687 AN: 151922 Hom.: 22237 Cov.: 31 AF XY: 0.533 AC XY: 39539 AN XY: 74244

African (AFR) AF: 0.564 AC: 23364 AN: 41422

American (AMR) AF: 0.548 AC: 8361 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1692 AN: 5160

South Asian (SAS) AF: 0.462 AC: 2219 AN: 4798

European-Finnish (FIN) AF: 0.433 AC: 4579 AN: 10564

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37978 AN: 67930

Other (OTH) AF: 0.499 AC: 1054 AN: 2112

Alfa AF: 0.548 Hom.: 74329

Bravo AF: 0.542

Asia WGS AF: 0.387 AC: 1343 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	1.8
DANN	Benign	0.76
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs6458065; hg19: chr6-38641354;