rs6926599

Variant names:

• chr6-33883084-G-A
• rs6926599
• ENST00000525912.2:n.698+10495C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-33883084-G-A
• chr6-33883084-G-T

Variant summary

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

The ENST00000525912.2(LINC01016):​n.698+10495C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.037 in 1,065,980 control chromosomes in the GnomAD database, including 1,490 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 0.066 (655 hom., cov: 32)
  • Exomes 𝑓: 0.032 (835 hom.)
• Consequence: LINC01016 ENST00000525912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 6 publications found

Genes affected

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

ANKRD36P2 (HGNC:56921):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 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	ENST00000525912.2	n.698+10495C>T		intron_variant	Intron 2 of 2	3
LINC01016	ENST00000656906.2	n.349+9612C>T		intron_variant	Intron 1 of 1
LINC01016	ENST00000661137.2	n.309+9233C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0655 AC: 9967 AN: 152132 Hom.: 655 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0583

GnomAD4 exome AF: 0.0322 AC: 29462 AN: 913730 Hom.: 835 AF XY: 0.0307 AC XY: 14261 AN XY: 465234

African (AFR) AF: 0.180 AC: 3596 AN: 20030

American (AMR) AF: 0.0235 AC: 463 AN: 19712

Ashkenazi Jewish (ASJ) AF: 0.00246 AC: 46 AN: 18726

East Asian (EAS) AF: 0.0000313 AC: 1 AN: 31978

South Asian (SAS) AF: 0.00280 AC: 173 AN: 61822

European-Finnish (FIN) AF: 0.0173 AC: 781 AN: 45162

Middle Eastern (MID) AF: 0.0147 AC: 42 AN: 2860

European-Non Finnish (NFE) AF: 0.0344 AC: 23146 AN: 673432

Other (OTH) AF: 0.0303 AC: 1214 AN: 40008

GnomAD4 genome AF: 0.0656 AC: 9984 AN: 152250 Hom.: 655 Cov.: 32 AF XY: 0.0623 AC XY: 4641 AN XY: 74458

African (AFR) AF: 0.164 AC: 6825 AN: 41516

American (AMR) AF: 0.0308 AC: 471 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4830

European-Finnish (FIN) AF: 0.0157 AC: 167 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0345 AC: 2349 AN: 68012

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0486 Hom.: 169

Bravo AF: 0.0705

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.77
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs6926599; hg19: chr6-33850861;