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 ENST00000749131.1(LINC00973):​n.396-16747A>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 ENST00000749131.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000749131.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00973	ENST00000474798.2	TSL:5	n.1119-16747A>T		intron	N/A
	LINC00973	ENST00000749131.1		n.396-16747A>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1481533;

hg19: chr3-99018079;