chr5-61768636-T-A

Variant names:

• chr5-61768636-T-A
• rs10514920
• ENST00000667197.1:n.813+12692T>A

Variant summary

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

The ENST00000667197.1(LINC03122):​n.813+12692T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 152,302 control chromosomes in the GnomAD database, including 44 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 0.021 (44 hom., cov: 32)
• Consequence: LINC03122 ENST00000667197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 1 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]

ENSG00000303846 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0207 (3157/152302) while in subpopulation AFR AF = 0.0346 (1438/41558). AF 95% confidence interval is 0.0331. There are 44 homozygotes in GnomAd4. There are 1664 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 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
LINC03122	ENST00000667197.1	n.813+12692T>A		intron_variant	Intron 6 of 6
LINC03122	ENST00000797193.1	n.570+12692T>A		intron_variant	Intron 5 of 10
LINC03122	ENST00000797195.1	n.347-12604T>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0207 AC: 3147 AN: 152184 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00981

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.00924

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0207 AC: 3157 AN: 152302 Hom.: 44 Cov.: 32 AF XY: 0.0223 AC XY: 1664 AN XY: 74484

African (AFR) AF: 0.0346 AC: 1438 AN: 41558

American (AMR) AF: 0.00980 AC: 150 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.00926 AC: 48 AN: 5184

South Asian (SAS) AF: 0.0340 AC: 164 AN: 4818

European-Finnish (FIN) AF: 0.0499 AC: 530 AN: 10622

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0113 AC: 766 AN: 68024

Other (OTH) AF: 0.0156 AC: 33 AN: 2116

Alfa AF: 0.0150 Hom.: 0

Bravo AF: 0.0178

Asia WGS AF: 0.0220 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.81
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs10514920; hg19: chr5-61064463;