rs947474

Variant names:

• chr10-6348488-G-A
• rs947474
• ENST00000659311.1:n.622+3708G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-6348488-G-A
• chr10-6348488-G-C
• chr10-6348488-G-T

Variant summary

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

The ENST00000659311.1(LINC02649):​n.622+3708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,142 control chromosomes in the GnomAD database, including 47,935 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 0.79 (47935 hom., cov: 32)
• Consequence: LINC02649 ENST00000659311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 89 publications found

Genes affected

LINC02649 (HGNC:54134): (long intergenic non-protein coding RNA 2649)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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
LINC02649	ENST00000659311.1	n.622+3708G>A		intron_variant	Intron 4 of 4
LINC02649	ENST00000783921.1	n.405+3708G>A		intron_variant	Intron 5 of 5
LINC02649	ENST00000783922.1	n.422+3708G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120433 AN: 152024 Hom.: 47907 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.792 AC: 120511 AN: 152142 Hom.: 47935 Cov.: 32 AF XY: 0.795 AC XY: 59115 AN XY: 74382

African (AFR) AF: 0.703 AC: 29140 AN: 41466

American (AMR) AF: 0.861 AC: 13165 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2855 AN: 3470

East Asian (EAS) AF: 0.882 AC: 4565 AN: 5178

South Asian (SAS) AF: 0.842 AC: 4061 AN: 4822

European-Finnish (FIN) AF: 0.820 AC: 8686 AN: 10594

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55355 AN: 68006

Other (OTH) AF: 0.803 AC: 1696 AN: 2112

Alfa AF: 0.807 Hom.: 200057

Bravo AF: 0.789

Asia WGS AF: 0.842 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.57
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs947474; hg19: chr10-6390450;