rs10498873

Variant names:

• chr6-70378113-G-C
• rs10498873
• ENST00000671572.2:n.89+2257G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-70378113-G-C
• chr6-70378113-G-T

Variant summary

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

The ENST00000671572.2(LINC01610):​n.89+2257G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 151,502 control chromosomes in the GnomAD database, including 4,031 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 0.21 (4031 hom., cov: 29)
• Consequence: LINC01610 ENST00000671572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 3 publications found

Genes affected

LINC01610 (HGNC:51676): (long intergenic non-protein coding RNA 1610)

ENSG00000310357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377848	XR_942670.2	n.141+3194C>G		intron_variant	Intron 1 of 3
LOC105377848	XR_942673.1	n.141+3194C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01610	ENST00000671572.2	n.89+2257G>C		intron_variant	Intron 1 of 6
ENSG00000310357	ENST00000849277.1	n.925+3194C>G		intron_variant	Intron 5 of 5
ENSG00000310357	ENST00000849278.1	n.490+3194C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32047 AN: 151384 Hom.: 4028 Cov.: 29

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.212 AC: 32082 AN: 151502 Hom.: 4031 Cov.: 29 AF XY: 0.212 AC XY: 15673 AN XY: 74030

African (AFR) AF: 0.354 AC: 14616 AN: 41252

American (AMR) AF: 0.176 AC: 2669 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1109 AN: 5136

South Asian (SAS) AF: 0.235 AC: 1124 AN: 4790

European-Finnish (FIN) AF: 0.158 AC: 1652 AN: 10478

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10056 AN: 67868

Other (OTH) AF: 0.183 AC: 386 AN: 2108

Alfa AF: 0.187 Hom.: 368

Bravo AF: 0.216

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.41
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs10498873; hg19: chr6-71087816; COSMIC: COSV69404384;