rs6468370

Positions:

• chr8-36567648-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.36567648C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253363	ENST00000524132.6	n.530-30172G>A		intron_variant		4
ENSG00000253363	ENST00000651399.1	n.517-71936G>A		intron_variant
ENSG00000253363	ENST00000656455.1	n.484+134173G>A		intron_variant

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

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.199

Alfa AF: 0.119 Hom.: 2689

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6468370; hg19: chr8-36425166;