rs171610

Variant names:

• chr5-5015072-T-C
• rs171610
• ENST00000509057.1:n.228+6557A>G

Variant summary

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

The ENST00000509057.1(ENSG00000251426):​n.228+6557A>G 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 152,166 control chromosomes in the GnomAD database, including 1,713 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 (1713 hom., cov: 32)
• Consequence: ENSG00000251426 ENST00000509057.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 1 publications found

Genes affected

ENSG00000251426 (HGNC:):

LINC01020 (HGNC:27968): (long intergenic non-protein coding RNA 1020)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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
ENSG00000251426	ENST00000509057.1	n.228+6557A>G		intron_variant	Intron 2 of 3	3
LINC01020	ENST00000659550.1	n.204+27080T>C		intron_variant	Intron 1 of 1
ENSG00000251426	ENST00000667766.1	n.201+6557A>G		intron_variant	Intron 2 of 2
ENSG00000251426	ENST00000715904.1	n.209+6557A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20731 AN: 152048 Hom.: 1702 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00991

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0437

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.136 AC: 20766 AN: 152166 Hom.: 1713 Cov.: 32 AF XY: 0.131 AC XY: 9775 AN XY: 74402

African (AFR) AF: 0.227 AC: 9412 AN: 41496

American (AMR) AF: 0.107 AC: 1639 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.0438 AC: 226 AN: 5162

South Asian (SAS) AF: 0.104 AC: 500 AN: 4824

European-Finnish (FIN) AF: 0.0590 AC: 626 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7663 AN: 68008

Other (OTH) AF: 0.142 AC: 300 AN: 2116

Alfa AF: 0.120 Hom.: 858

Bravo AF: 0.144

Asia WGS AF: 0.119 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.1
DANN	Benign	0.65
PhyloP100		0.091
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs171610; hg19: chr5-5015185;