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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671572.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01610	ENST00000671572.2		n.89+2257G>C		intron	N/A
	ENSG00000310357	ENST00000849277.1		n.925+3194C>G		intron	N/A
	ENSG00000310357	ENST00000849278.1		n.490+3194C>G		intron	N/A

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 v4.9

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;