rs10504895

Positions:

• chr8-90532649-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665012.1(ENSG00000254180):​n.542+1893G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 152,150 control chromosomes in the GnomAD database, including 101 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 0.034 (101 hom., cov: 32)
• Consequence: ENST00000665012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

Genes affected

(HGNC:):

LINC00534 (HGNC:43643): (long intergenic non-protein coding RNA 534)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901975	XR_007061002.1	n.443+1893G>A		intron_variant, non_coding_transcript_variant
LOC124901975	XR_007061003.1	n.513+1893G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665012.1	n.542+1893G>A		intron_variant, non_coding_transcript_variant
LINC00534	ENST00000667296.1	n.456+78126C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0344 AC: 5231 AN: 152034 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0345 AC: 5243 AN: 152150 Hom.: 101 Cov.: 32 AF XY: 0.0326 AC XY: 2423 AN XY: 74382

Gnomad4 AFR AF: 0.0564

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.0171

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0340 Hom.: 14

Bravo AF: 0.0356

Asia WGS AF: 0.00549 AC: 20 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504895; hg19: chr8-91544877;