rs6468370

Variant names:

• chr8-36567648-C-T
• rs6468370
• ENST00000524132.6:n.530-30172G>A

Variant summary

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

The ENST00000524132.6(ENSG00000253363):​n.530-30172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,966 control chromosomes in the GnomAD database, including 4,985 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 0.21 (4985 hom., cov: 32)
• Consequence: ENSG00000253363 ENST00000524132.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 4 publications found

Genes affected

ENSG00000253363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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
ENSG00000253363	ENST00000524132.6	n.530-30172G>A		intron_variant	Intron 4 of 4	4
ENSG00000253363	ENST00000651399.1	n.517-71936G>A		intron_variant	Intron 4 of 5
ENSG00000253363	ENST00000656455.2	n.484+134173G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31637 AN: 151848 Hom.: 4954 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.209 AC: 31720 AN: 151966 Hom.: 4985 Cov.: 32 AF XY: 0.210 AC XY: 15590 AN XY: 74284

African (AFR) AF: 0.437 AC: 18094 AN: 41446

American (AMR) AF: 0.141 AC: 2144 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3466

East Asian (EAS) AF: 0.270 AC: 1391 AN: 5146

South Asian (SAS) AF: 0.252 AC: 1211 AN: 4804

European-Finnish (FIN) AF: 0.106 AC: 1123 AN: 10578

Middle Eastern (MID) AF: 0.183 AC: 53 AN: 290

European-Non Finnish (NFE) AF: 0.100 AC: 6828 AN: 67968

Other (OTH) AF: 0.199 AC: 419 AN: 2106

Alfa AF: 0.140 Hom.: 6740

Bravo AF: 0.217

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.092
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6468370; hg19: chr8-36425166;