rs16972414

Variant names:

• chr18-39875958-A-G
• rs16972414
• ENST00000585822.1:n.310+346T>C

Variant summary

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

The ENST00000660142.1(LINC01902):​n.592A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,786 control chromosomes in the GnomAD database, including 5,174 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 0.24 (5174 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01902 ENST00000660142.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 1 publications found

Genes affected

LINC01901 (HGNC:52720): (long intergenic non-protein coding RNA 1901)

LINC01902 (HGNC:52721): (long intergenic non-protein coding RNA 1902)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660142.1. 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
	LINC01902	NR_151703.1		n.822-430A>G		intron	N/A
	LINC01901	NR_187474.1		n.246-13709T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01901	ENST00000585822.1	TSL:1	n.310+346T>C		intron	N/A
	LINC01902	ENST00000636467.3	TSL:5	n.5857A>G		non_coding_transcript_exon	Exon 6 of 7
	LINC01902	ENST00000660142.1		n.592A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37088 AN: 151668 Hom.: 5179 Cov.: 31

Gnomad AFR AF: 0.0965

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.259

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.244 AC: 37090 AN: 151786 Hom.: 5174 Cov.: 31 AF XY: 0.247 AC XY: 18284 AN XY: 74126

African (AFR) AF: 0.0965 AC: 3998 AN: 41442

American (AMR) AF: 0.283 AC: 4316 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1509 AN: 5130

South Asian (SAS) AF: 0.369 AC: 1771 AN: 4794

European-Finnish (FIN) AF: 0.307 AC: 3211 AN: 10474

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.298 AC: 20206 AN: 67912

Other (OTH) AF: 0.261 AC: 549 AN: 2100

Alfa AF: 0.265 Hom.: 2073

Bravo AF: 0.232

Asia WGS AF: 0.352 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.035
DANN	Benign	0.54
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs16972414; hg19: chr18-37455922;