4-137213427-A-G

Variant names:

• chr4-137213427-A-G
• rs10519410
• ENST00000828076.1:n.591+16013A>G

Variant summary

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

The ENST00000828076.1(LINC02510):​n.591+16013A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,354 control chromosomes in the GnomAD database, including 3,485 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 0.21 (3485 hom., cov: 32)
• Consequence: LINC02510 ENST00000828076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 15 publications found

Genes affected

LINC02510 (HGNC:53499): (long intergenic non-protein coding RNA 2510)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 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
LINC02510	ENST00000828076.1	n.591+16013A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31433 AN: 151234 Hom.: 3480 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.208 AC: 31449 AN: 151354 Hom.: 3485 Cov.: 32 AF XY: 0.209 AC XY: 15447 AN XY: 73968

African (AFR) AF: 0.242 AC: 10007 AN: 41330

American (AMR) AF: 0.179 AC: 2706 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1145 AN: 3444

East Asian (EAS) AF: 0.227 AC: 1166 AN: 5136

South Asian (SAS) AF: 0.317 AC: 1528 AN: 4814

European-Finnish (FIN) AF: 0.148 AC: 1567 AN: 10580

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12699 AN: 67630

Other (OTH) AF: 0.220 AC: 461 AN: 2094

Alfa AF: 0.206 Hom.: 3446

Bravo AF: 0.207

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10519410; hg19: chr4-138134581;