rs171610

Positions:

• chr5-5015072-T-C

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, non coding transcript 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: ENST00000509057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000509057.1	n.228+6557A>G		intron_variant, non_coding_transcript_variant		3
LINC01020	ENST00000659550.1	n.204+27080T>C		intron_variant, non_coding_transcript_variant
	ENST00000667766.1	n.201+6557A>G		intron_variant, non_coding_transcript_variant

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;