rs10162002

Variant names:

• chr13-23468371-G-A
• rs10162002
• ENST00000575689.4:n.593+1208G>A

Variant summary

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

The ENST00000575689.4(LINC00327):​n.593+1208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,088 control chromosomes in the GnomAD database, including 3,366 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 0.19 (3366 hom., cov: 33)
• Consequence: LINC00327 ENST00000575689.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 9 publications found

Genes affected

LINC00327 (HGNC:42009): (long intergenic non-protein coding RNA 327)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000575689.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00327	ENST00000575689.4	TSL:1	n.593+1208G>A		intron	N/A
	LINC00327	ENST00000576696.2	TSL:1	n.1179+622G>A		intron	N/A
	LINC00327	ENST00000655268.1		n.145-2143G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29102 AN: 151970 Hom.: 3349 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.192 AC: 29148 AN: 152088 Hom.: 3366 Cov.: 33 AF XY: 0.189 AC XY: 14028 AN XY: 74348

African (AFR) AF: 0.326 AC: 13521 AN: 41480

American (AMR) AF: 0.151 AC: 2316 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3464

East Asian (EAS) AF: 0.110 AC: 567 AN: 5174

South Asian (SAS) AF: 0.0849 AC: 409 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1212 AN: 10560

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9750 AN: 67986

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.159 Hom.: 8624

Bravo AF: 0.201

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.20
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10162002; hg19: chr13-24042510;