rs1475084

Positions:

• chr10-62845974-G-A

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 0.479 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.62845974G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289487	ENST00000493899.2	n.542-30005C>T		intron_variant		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

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.477

Alfa AF: 0.512 Hom.: 9184

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1475084; hg19: chr10-64605734;