ENST00000505623.5:n.124+1672C>T

Variant names:

• chr5-61675951-G-A
• rs410850
• ENST00000505623.5:n.124+1672C>T

Variant summary

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

The ENST00000505623.5(ENSG00000248529):​n.124+1672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,004 control chromosomes in the GnomAD database, including 9,812 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 0.36 (9812 hom., cov: 32)
• Consequence: ENSG00000248529 ENST00000505623.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 3 publications found

Genes affected

ENSG00000248529 (HGNC:58412):

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]

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 = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03152	NR_109910.1	n.1161+1672C>T		intron_variant	Intron 6 of 7
LINC03122	NR_126523.1	n.141-27915G>A		intron_variant	Intron 2 of 2
LINC03122	NR_126524.1	n.141-27915G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248529	ENST00000505623.5	n.124+1672C>T		intron_variant	Intron 2 of 4	1
ENSG00000248529	ENST00000507264.6	n.178+1672C>T		intron_variant	Intron 2 of 2	1
ENSG00000248529	ENST00000513386.1	n.1161+1672C>T		intron_variant	Intron 6 of 7	1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54166 AN: 151886 Hom.: 9807 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.357 AC: 54206 AN: 152004 Hom.: 9812 Cov.: 32 AF XY: 0.359 AC XY: 26648 AN XY: 74272

African (AFR) AF: 0.386 AC: 16001 AN: 41464

American (AMR) AF: 0.287 AC: 4392 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1641 AN: 5148

South Asian (SAS) AF: 0.296 AC: 1427 AN: 4824

European-Finnish (FIN) AF: 0.422 AC: 4451 AN: 10550

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24247 AN: 67954

Other (OTH) AF: 0.340 AC: 717 AN: 2110

Alfa AF: 0.341 Hom.: 15072

Bravo AF: 0.344

Asia WGS AF: 0.364 AC: 1267 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	0.0070
DANN	Benign	0.79
PhyloP100		-2.9
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: rs410850; hg19: chr5-60971778;