rs10504741

Variant names:

• chr8-81843118-C-A
• rs10504741
• ENST00000647805.1:n.273+228C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-81843118-C-A
• chr8-81843118-C-G
• chr8-81843118-C-T

Variant summary

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

The ENST00000647805.1(LINC02235):​n.273+228C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,088 control chromosomes in the GnomAD database, including 27,746 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 0.60 (27746 hom., cov: 33)
• Consequence: LINC02235 ENST00000647805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 10 publications found

Genes affected

LINC02235 (HGNC:53106): (long intergenic non-protein coding RNA 2235)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02235	NR_170312.1	n.53+447C>A		intron_variant	Intron 1 of 3
LINC02235	NR_170313.1	n.53+447C>A		intron_variant	Intron 1 of 3
LINC02235	NR_170314.1	n.53+447C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02235	ENST00000647805.1	n.273+228C>A		intron_variant	Intron 1 of 6
LINC02235	ENST00000658926.1	n.59+447C>A		intron_variant	Intron 1 of 5
LINC02235	ENST00000660458.1	n.56+447C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90610 AN: 151970 Hom.: 27733 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.596 AC: 90661 AN: 152088 Hom.: 27746 Cov.: 33 AF XY: 0.604 AC XY: 44899 AN XY: 74340

African (AFR) AF: 0.512 AC: 21237 AN: 41454

American (AMR) AF: 0.650 AC: 9939 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2060 AN: 3468

East Asian (EAS) AF: 0.980 AC: 5072 AN: 5178

South Asian (SAS) AF: 0.667 AC: 3220 AN: 4828

European-Finnish (FIN) AF: 0.707 AC: 7467 AN: 10558

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39680 AN: 67994

Other (OTH) AF: 0.588 AC: 1240 AN: 2108

Alfa AF: 0.574 Hom.: 3828

Bravo AF: 0.592

Asia WGS AF: 0.811 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.42
PhyloP100		-0.10
PromoterAI		0.0034	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10504741; hg19: chr8-82755353;