rs6468418

Positions:

• chr8-37611531-T-C
• chr8-37611531-T-G

Variant summary

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

The ENST00000517714.1(ENSG00000254306):​n.136-8112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,020 control chromosomes in the GnomAD database, including 20,451 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 0.52 (20451 hom., cov: 32)
• Consequence: ENSG00000254306 ENST00000517714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

Genes affected

ENSG00000254306 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379380	XR_949685.3	n.272-8112A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254306	ENST00000517714.1	n.136-8112A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78652 AN: 151902 Hom.: 20433 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.518 AC: 78709 AN: 152020 Hom.: 20451 Cov.: 32 AF XY: 0.523 AC XY: 38848 AN XY: 74312

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.500

Alfa AF: 0.517 Hom.: 27452

Bravo AF: 0.513

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6468418; hg19: chr8-37469049;