chr10-62820815-C-T

Variant names:

• chr10-62820815-C-T
• rs224278
• ENST00000493899.2:n.542-4846G>A

Variant summary

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

The ENST00000493899.2(ENSG00000289487):​n.542-4846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,136 control chromosomes in the GnomAD database, including 12,419 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 (12419 hom., cov: 33)
• Consequence: ENSG00000289487 ENST00000493899.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 21 publications found

Genes affected

ENSG00000289487 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493899.2. 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
	ENSG00000289487	ENST00000493899.2	TSL:5	n.542-4846G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59660 AN: 152018 Hom.: 12411 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.392 AC: 59683 AN: 152136 Hom.: 12419 Cov.: 33 AF XY: 0.398 AC XY: 29571 AN XY: 74370

African (AFR) AF: 0.265 AC: 10993 AN: 41498

American (AMR) AF: 0.477 AC: 7291 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3470

East Asian (EAS) AF: 0.579 AC: 3001 AN: 5180

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4826

European-Finnish (FIN) AF: 0.505 AC: 5329 AN: 10560

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28068 AN: 68002

Other (OTH) AF: 0.394 AC: 832 AN: 2110

Alfa AF: 0.406 Hom.: 36494

Bravo AF: 0.391

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs224278; hg19: chr10-64580575;