rs10493510

Variant names:

• chr1-72745942-A-C
• rs10493510
• ENST00000654386.1:n.436+3224T>G

Variant summary

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

The ENST00000654386.1(ENSG00000225087):​n.436+3224T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,100 control chromosomes in the GnomAD database, including 1,584 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 0.084 (1584 hom., cov: 32)
• Consequence: ENSG00000225087 ENST00000654386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 0 publications found

Genes affected

ENSG00000225087 (HGNC:):

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378798	NR_188684.1	n.202+3224T>G		intron_variant	Intron 2 of 4
LOC105378798	NR_188685.1	n.230+3224T>G		intron_variant	Intron 3 of 4
LOC105378798	NR_188686.1	n.202+3224T>G		intron_variant	Intron 2 of 3
LOC105378798	NR_188687.1	n.202+3224T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225087	ENST00000654386.1	n.436+3224T>G		intron_variant	Intron 3 of 3
ENSG00000225087	ENST00000660076.1	n.207+3224T>G		intron_variant	Intron 2 of 2
ENSG00000225087	ENST00000661739.1	n.202+3224T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12759 AN: 151982 Hom.: 1583 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.00703

Gnomad FIN AF: 0.00574

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00874

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0841 AC: 12790 AN: 152100 Hom.: 1584 Cov.: 32 AF XY: 0.0809 AC XY: 6017 AN XY: 74368

African (AFR) AF: 0.274 AC: 11368 AN: 41460

American (AMR) AF: 0.0328 AC: 500 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3472

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5160

South Asian (SAS) AF: 0.00704 AC: 34 AN: 4832

European-Finnish (FIN) AF: 0.00574 AC: 61 AN: 10632

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00874 AC: 594 AN: 67984

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0643 Hom.: 157

Bravo AF: 0.0954

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.49
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10493510; hg19: chr1-73211625;