rs10508271

Variant names:

• chr10-3936512-G-C
• rs10508271
• ENST00000692986.2:n.196-4699G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-3936512-G-C
• chr10-3936512-G-T

Variant summary

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

The ENST00000692986.2(LINC02660):​n.196-4699G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,170 control chromosomes in the GnomAD database, including 1,126 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 0.074 (1126 hom., cov: 32)
• Consequence: LINC02660 ENST00000692986.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 0 publications found

Genes affected

LINC02660 (HGNC:54146): (long intergenic non-protein coding RNA 2660)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02660	ENST00000692986.2	n.196-4699G>C		intron_variant	Intron 1 of 1
LINC02660	ENST00000724600.1	n.167-11997G>C		intron_variant	Intron 1 of 1
LINC02660	ENST00000724601.1	n.68-4699G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0734 AC: 11158 AN: 152050 Hom.: 1116 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.00320

Gnomad OTH AF: 0.0633

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

GnomAD4 genome AF: 0.0736 AC: 11199 AN: 152170 Hom.: 1126 Cov.: 32 AF XY: 0.0729 AC XY: 5423 AN XY: 74420

African (AFR) AF: 0.221 AC: 9162 AN: 41454

American (AMR) AF: 0.0847 AC: 1296 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3466

East Asian (EAS) AF: 0.0220 AC: 114 AN: 5190

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4830

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10606

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00320 AC: 218 AN: 68020

Other (OTH) AF: 0.0641 AC: 135 AN: 2106

Alfa AF: 0.0140 Hom.: 21

Bravo AF: 0.0875

Asia WGS AF: 0.0490 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.031
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10508271; hg19: chr10-3978704;