chr5-124228271-C-T

Variant names:

• chr5-124228271-C-T
• rs10070979
• ENST00000628324.2:n.402+157958G>A

Variant summary

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

The ENST00000628324.2(LINC01170):​n.402+157958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,060 control chromosomes in the GnomAD database, including 4,112 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 0.20 (4112 hom., cov: 32)
• Consequence: LINC01170 ENST00000628324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 2 publications found

Genes affected

LINC01170 (HGNC:49542): (long intergenic non-protein coding RNA 1170)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000628324.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01170	NR_125774.1		n.489+157958G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01170	ENST00000628324.2	TSL:2	n.402+157958G>A		intron	N/A
	LINC01170	ENST00000653233.2		n.499+89378G>A		intron	N/A
	LINC01170	ENST00000657766.2		n.393+77905G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29582 AN: 151942 Hom.: 4070 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.0543

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.195 AC: 29683 AN: 152060 Hom.: 4112 Cov.: 32 AF XY: 0.196 AC XY: 14593 AN XY: 74338

African (AFR) AF: 0.370 AC: 15340 AN: 41426

American (AMR) AF: 0.175 AC: 2668 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 539 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1957 AN: 5158

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4826

European-Finnish (FIN) AF: 0.0543 AC: 575 AN: 10594

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6814 AN: 67988

Other (OTH) AF: 0.187 AC: 395 AN: 2112

Alfa AF: 0.155 Hom.: 453

Bravo AF: 0.212

Asia WGS AF: 0.333 AC: 1160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10070979; hg19: chr5-123563964;