chr17-69981276-T-C

Variant names:

• chr17-69981276-T-C
• rs180051
• ENST00000420427.3:n.498T>C

Variant summary

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

The ENST00000420427.3(LINC01497):​n.498T>C 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 0.19 in 152,018 control chromosomes in the GnomAD database, including 3,189 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 (3188 hom., cov: 32)
  • Exomes 𝑓: 0.39 (1 hom.)
• Consequence: LINC01497 ENST00000420427.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 1 publications found

Genes affected

LINC01497 (HGNC:51163): (long intergenic non-protein coding RNA 1497)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420427.3. 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
	LINC01497	NR_110874.1		n.335T>C		non_coding_transcript_exon	Exon 3 of 5
	LINC01497	NR_110875.1		n.308T>C		non_coding_transcript_exon	Exon 3 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01497	ENST00000420427.3	TSL:3	n.498T>C		non_coding_transcript_exon	Exon 3 of 5
	LINC01497	ENST00000455460.7	TSL:3	n.471T>C		non_coding_transcript_exon	Exon 3 of 5
	LINC01497	ENST00000649355.1		n.368T>C		non_coding_transcript_exon	Exon 3 of 8

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28874 AN: 151882 Hom.: 3184 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0620

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.180

GnomAD4 exome AF: 0.389 AC: 7 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.375 AC XY: 6 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.625 AC: 5 AN: 8

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.190 AC: 28905 AN: 152000 Hom.: 3188 Cov.: 32 AF XY: 0.183 AC XY: 13600 AN XY: 74302

African (AFR) AF: 0.305 AC: 12628 AN: 41434

American (AMR) AF: 0.161 AC: 2448 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3466

East Asian (EAS) AF: 0.0160 AC: 83 AN: 5182

South Asian (SAS) AF: 0.0626 AC: 302 AN: 4822

European-Finnish (FIN) AF: 0.0956 AC: 1012 AN: 10588

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11482 AN: 67964

Other (OTH) AF: 0.177 AC: 373 AN: 2104

Alfa AF: 0.179 Hom.: 3956

Bravo AF: 0.200

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.73
PhyloP100		1.0
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs180051; hg19: chr17-67977417;