3-99299235-A-T

Variant names:

• chr3-99299235-A-T
• rs1481533
• ENST00000474798.2:n.1119-16747A>T

Variant summary

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

The ENST00000474798.2(LINC00973):​n.1119-16747A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,026 control chromosomes in the GnomAD database, including 62,233 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 0.90 (62233 hom., cov: 31)
• Consequence: LINC00973 ENST00000474798.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 0 publications found

Genes affected

LINC00973 (HGNC:48868): (long intergenic non-protein coding RNA 973)

LOC124909399 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909399	XR_007095979.1	n.125-16747A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00973	ENST00000474798.2	n.1119-16747A>T		intron_variant	Intron 10 of 10	5
LINC00973	ENST00000749131.1	n.396-16747A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136468 AN: 151908 Hom.: 62216 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.898 AC: 136530 AN: 152026 Hom.: 62233 Cov.: 31 AF XY: 0.894 AC XY: 66421 AN XY: 74302

African (AFR) AF: 0.736 AC: 30528 AN: 41452

American (AMR) AF: 0.903 AC: 13756 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3374 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4417 AN: 5172

South Asian (SAS) AF: 0.860 AC: 4144 AN: 4820

European-Finnish (FIN) AF: 0.934 AC: 9905 AN: 10606

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67253 AN: 67948

Other (OTH) AF: 0.927 AC: 1955 AN: 2108

Alfa AF: 0.950 Hom.: 3377

Bravo AF: 0.889

Asia WGS AF: 0.862 AC: 2991 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.64
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1481533; hg19: chr3-99018079;