10-85393840-T-A

Position:

• chr10-85393840-T-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 0.49 in 149,882 control chromosomes in the GnomAD database, including 18,154 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 0.49 (18154 hom., cov: 27)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85393840T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02647	ENST00000655477.1	n.465-14892A>T		intron_variant
LINC02647	ENST00000658106.1	n.374-14892A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.490 AC: 73433 AN: 149774 Hom.: 18123 Cov.: 27

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.490 AC: 73500 AN: 149882 Hom.: 18154 Cov.: 27 AF XY: 0.490 AC XY: 35809 AN XY: 73150

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.502

Alfa AF: 0.468 Hom.: 2071

Bravo AF: 0.497

Asia WGS AF: 0.444 AC: 1544 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11596082; hg19: chr10-87153596;