5-61654384-T-G

Variant names:

• chr5-61654384-T-G
• rs11738335
• ENST00000505642.6:n.148+10984T>G

Variant summary

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

The ENST00000505642.6(LINC03122):​n.148+10984T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,858 control chromosomes in the GnomAD database, including 3,867 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 0.22 (3867 hom., cov: 31)
• Consequence: LINC03122 ENST00000505642.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 13 publications found

Genes affected

LINC03122 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000248529 (HGNC:58412):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03122	NR_126523.1	n.140+10984T>G		intron_variant	Intron 2 of 2
LINC03122	NR_126524.1	n.140+10984T>G		intron_variant	Intron 2 of 3
LINC03122	NR_126525.1	n.66+16538T>G		intron_variant	Intron 1 of 1
LINC03122	NR_161251.1	n.161+10984T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03122	ENST00000505642.6	n.148+10984T>G		intron_variant	Intron 2 of 3	2
LINC03122	ENST00000507461.2	n.139+16538T>G		intron_variant	Intron 1 of 4	4
LINC03122	ENST00000510414.4	n.161+10984T>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32941 AN: 151762 Hom.: 3862 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.217 AC: 32986 AN: 151858 Hom.: 3867 Cov.: 31 AF XY: 0.217 AC XY: 16138 AN XY: 74198

African (AFR) AF: 0.320 AC: 13246 AN: 41376

American (AMR) AF: 0.163 AC: 2495 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3468

East Asian (EAS) AF: 0.127 AC: 655 AN: 5172

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4806

European-Finnish (FIN) AF: 0.213 AC: 2237 AN: 10510

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12091 AN: 67946

Other (OTH) AF: 0.204 AC: 430 AN: 2104

Alfa AF: 0.184 Hom.: 8929

Bravo AF: 0.214

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.57
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11738335; hg19: chr5-60950211;