rs35691538

Variant names:

• chr8-125701794-G-A
• rs35691538
• ENST00000651999.1:n.211+21750G>A

Variant summary

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

The ENST00000651999.1(LINC02964):​n.211+21750G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 151,972 control chromosomes in the GnomAD database, including 1,161 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 0.084 (1161 hom., cov: 32)
• Consequence: LINC02964 ENST00000651999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• Publications: 1 publications found

Genes affected

LINC02964 (HGNC:53487): (long intergenic non-protein coding RNA 2964)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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
LINC02964	ENST00000651999.1	n.211+21750G>A		intron_variant	Intron 4 of 7
LINC02964	ENST00000816149.1	n.254+21750G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0837 AC: 12704 AN: 151854 Hom.: 1157 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0604

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.00869

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0262

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0838 AC: 12729 AN: 151972 Hom.: 1161 Cov.: 32 AF XY: 0.0805 AC XY: 5979 AN XY: 74306

African (AFR) AF: 0.226 AC: 9337 AN: 41388

American (AMR) AF: 0.0504 AC: 769 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0604 AC: 209 AN: 3462

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5164

South Asian (SAS) AF: 0.0404 AC: 195 AN: 4822

European-Finnish (FIN) AF: 0.00869 AC: 92 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0262 AC: 1783 AN: 67974

Other (OTH) AF: 0.0752 AC: 158 AN: 2100

Alfa AF: 0.0609 Hom.: 92

Bravo AF: 0.0943

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.48
DANN	Benign	0.67
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs35691538; hg19: chr8-126714038;