rs2495975

Variant names:

• chr6-33976237-T-C
• rs2495975
• ENST00000799599.1:n.207+5643A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-33976237-T-C
• chr6-33976237-T-G

Variant summary

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

The ENST00000799599.1(LINC01016):​n.207+5643A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,120 control chromosomes in the GnomAD database, including 44,838 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 0.77 (44838 hom., cov: 32)
• Consequence: LINC01016 ENST00000799599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 11 publications found

Genes affected

LINC01016 (HGNC:48991): (long intergenic non-protein coding RNA 1016)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 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
LINC01016	ENST00000799599.1	n.207+5643A>G		intron_variant	Intron 2 of 3
LINC01016	ENST00000799600.1	n.136+5643A>G		intron_variant	Intron 2 of 4
LINC01016	ENST00000799601.1	n.175+5643A>G		intron_variant	Intron 2 of 5
LINC01016	ENST00000799602.1	n.175+5643A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116612 AN: 152002 Hom.: 44800 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.767 AC: 116709 AN: 152120 Hom.: 44838 Cov.: 32 AF XY: 0.770 AC XY: 57282 AN XY: 74354

African (AFR) AF: 0.736 AC: 30521 AN: 41490

American (AMR) AF: 0.753 AC: 11519 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2773 AN: 3472

East Asian (EAS) AF: 0.843 AC: 4338 AN: 5148

South Asian (SAS) AF: 0.870 AC: 4197 AN: 4824

European-Finnish (FIN) AF: 0.789 AC: 8359 AN: 10598

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52554 AN: 67970

Other (OTH) AF: 0.752 AC: 1589 AN: 2114

Alfa AF: 0.773 Hom.: 115474

Bravo AF: 0.761

Asia WGS AF: 0.838 AC: 2915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.20
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2495975; hg19: chr6-33944014;