chr10-62845974-G-A

Variant names:

• chr10-62845974-G-A
• rs1475084
• ENST00000493899.2:n.542-30005C>T

Variant summary

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

The ENST00000493899.2(ENSG00000289487):​n.542-30005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,010 control chromosomes in the GnomAD database, including 17,597 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 0.48 (17597 hom., cov: 32)
• Consequence: ENSG00000289487 ENST00000493899.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.513 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
ENSG00000289487	ENST00000493899.2	n.542-30005C>T		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72772 AN: 151892 Hom.: 17584 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.479 AC: 72833 AN: 152010 Hom.: 17597 Cov.: 32 AF XY: 0.483 AC XY: 35882 AN XY: 74308

African (AFR) AF: 0.434 AC: 17980 AN: 41444

American (AMR) AF: 0.420 AC: 6409 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1642 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2028 AN: 5176

South Asian (SAS) AF: 0.492 AC: 2372 AN: 4824

European-Finnish (FIN) AF: 0.532 AC: 5613 AN: 10548

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

European-Non Finnish (NFE) AF: 0.518 AC: 35176 AN: 67958

Other (OTH) AF: 0.477 AC: 1006 AN: 2110

Alfa AF: 0.511 Hom.: 10231

Bravo AF: 0.465

Asia WGS AF: 0.470 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs1475084; hg19: chr10-64605734;