rs171610

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509057.1(ENSG00000250481):​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: ENSG00000250481 ENST00000509057.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

ENSG00000250481 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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
ENSG00000250481	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
ENSG00000250481	ENST00000667766.1	n.201+6557A>G		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0438

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.142

Alfa AF: 0.122 Hom.: 568

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs171610; hg19: chr5-5015185;