rs1455528

Variant names:

• chr17-41554594-C-G
• rs1455528
• ENST00000456403.1:n.-99G>C

Variant summary

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

The ENST00000456403.1(LINC00974):​n.-99G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 151,950 control chromosomes in the GnomAD database, including 68,990 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 0.95 (68977 hom., cov: 27)
  • Exomes 𝑓: 0.96 (13 hom.)
• Consequence: LINC00974 ENST00000456403.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 1 publications found

Genes affected

LINC00974 (HGNC:27105): (long intergenic non-protein coding RNA 974)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00974	NR_038442.1	n.-99G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00974	ENST00000456403.1	n.-99G>C		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144375 AN: 151804 Hom.: 68949 Cov.: 27

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.959

GnomAD4 exome AF: 0.964 AC: 27 AN: 28 Hom.: 13 AF XY: 0.955 AC XY: 21 AN XY: 22

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: 0.964 AC: 27 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.951 AC: 144455 AN: 151922 Hom.: 68977 Cov.: 27 AF XY: 0.952 AC XY: 70682 AN XY: 74258

African (AFR) AF: 0.846 AC: 34963 AN: 41332

American (AMR) AF: 0.978 AC: 14958 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3463 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5139 AN: 5142

South Asian (SAS) AF: 0.987 AC: 4731 AN: 4794

European-Finnish (FIN) AF: 0.997 AC: 10554 AN: 10586

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67431 AN: 67992

Other (OTH) AF: 0.957 AC: 2016 AN: 2106

Alfa AF: 0.969 Hom.: 8886

Bravo AF: 0.944

Asia WGS AF: 0.971 AC: 3377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1455528; hg19: chr17-39710846;