8-62143109-C-T

Variant names:

• chr8-62143109-C-T
• rs900493
• ENST00000833950.1:n.251-7363G>A

Variant summary

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

The ENST00000833950.1(ENSG00000308421):​n.251-7363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,658 control chromosomes in the GnomAD database, including 12,128 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 0.39 (12128 hom., cov: 30)
• Consequence: ENSG00000308421 ENST00000833950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 3 publications found

Genes affected

ENSG00000308421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833950.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308421	ENST00000833950.1		n.251-7363G>A		intron	N/A
	ENSG00000237810	ENST00000518921.1	TSL:6	n.*202G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58687 AN: 151538 Hom.: 12126 Cov.: 30

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.387 AC: 58691 AN: 151658 Hom.: 12128 Cov.: 30 AF XY: 0.390 AC XY: 28891 AN XY: 74074

African (AFR) AF: 0.247 AC: 10186 AN: 41318

American (AMR) AF: 0.396 AC: 6033 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1420 AN: 5120

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4814

European-Finnish (FIN) AF: 0.538 AC: 5639 AN: 10476

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30710 AN: 67900

Other (OTH) AF: 0.385 AC: 810 AN: 2104

Alfa AF: 0.419 Hom.: 37037

Bravo AF: 0.365

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.84
DANN	Benign	0.41
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs900493; hg19: chr8-63055668; COSMIC: COSV72962419;