rs9536962

Variant names:

• chr13-55104801-G-A
• rs9536962
• ENST00000616578.2:n.222-1969G>A

Variant summary

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

The ENST00000616578.2(LINC02335):​n.222-1969G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,944 control chromosomes in the GnomAD database, including 1,677 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 0.14 (1677 hom., cov: 31)
• Consequence: LINC02335 ENST00000616578.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 3 publications found

Genes affected

LINC02335 (HGNC:53255): (long intergenic non-protein coding RNA 2335)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02335	NR_186625.1	n.784-1969G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02335	ENST00000616578.2	n.222-1969G>A		intron_variant	Intron 2 of 3	3
LINC02335	ENST00000732192.1	n.221-1969G>A		intron_variant	Intron 2 of 5
LINC02335	ENST00000732193.1	n.317+41799G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20597 AN: 151826 Hom.: 1664 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.136 AC: 20643 AN: 151944 Hom.: 1677 Cov.: 31 AF XY: 0.137 AC XY: 10173 AN XY: 74244

African (AFR) AF: 0.203 AC: 8417 AN: 41422

American (AMR) AF: 0.208 AC: 3170 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0783 AC: 271 AN: 3462

East Asian (EAS) AF: 0.0971 AC: 500 AN: 5148

South Asian (SAS) AF: 0.104 AC: 500 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1222 AN: 10562

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0921 AC: 6262 AN: 67970

Other (OTH) AF: 0.118 AC: 249 AN: 2110

Alfa AF: 0.109 Hom.: 2141

Bravo AF: 0.147

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs9536962; hg19: chr13-55678936;