chr6-33968126-T-C

Variant names:

• chr6-33968126-T-C
• rs9469655
• ENST00000799599.1:n.207+13754A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000799599.1(LINC01016):​n.207+13754A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 152,230 control chromosomes in the GnomAD database, including 35 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 0.014 (35 hom., cov: 32)
• Consequence: LINC01016 ENST00000799599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 3 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=-0.84).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0138 (2102/152230) while in subpopulation AFR AF = 0.0379 (1574/41528). AF 95% confidence interval is 0.0363. There are 35 homozygotes in GnomAd4. There are 988 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 35 gene

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+13754A>G		intron_variant	Intron 2 of 3
LINC01016	ENST00000799600.1	n.136+13754A>G		intron_variant	Intron 2 of 4
LINC01016	ENST00000799601.1	n.175+13754A>G		intron_variant	Intron 2 of 5
LINC01016	ENST00000799602.1	n.175+13754A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0137 AC: 2088 AN: 152112 Hom.: 34 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00766

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00388

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0138 AC: 2102 AN: 152230 Hom.: 35 Cov.: 32 AF XY: 0.0133 AC XY: 988 AN XY: 74434

African (AFR) AF: 0.0379 AC: 1574 AN: 41528

American (AMR) AF: 0.00765 AC: 117 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.00312 AC: 15 AN: 4812

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00388 AC: 264 AN: 68018

Other (OTH) AF: 0.0166 AC: 35 AN: 2112

Alfa AF: 0.00646 Hom.: 5

Bravo AF: 0.0158

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.78
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9469655; hg19: chr6-33935903;