10-85393883-A-G

Position:

• chr10-85393883-A-G

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 0.48 in 150,600 control chromosomes in the GnomAD database, including 17,461 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 (17461 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85393883A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02647	ENST00000655477.1	n.465-14935T>C		intron_variant
LINC02647	ENST00000658106.1	n.374-14935T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72219 AN: 150488 Hom.: 17438 Cov.: 28

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.480 AC: 72276 AN: 150600 Hom.: 17461 Cov.: 28 AF XY: 0.479 AC XY: 35270 AN XY: 73588

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.489

Alfa AF: 0.464 Hom.: 2722

Bravo AF: 0.488

Asia WGS AF: 0.440 AC: 1534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7089868; hg19: chr10-87153639;