rs1383840

Variant names:

• chr3-99313295-G-A
• rs1383840
• ENST00000474798.2:n.1119-2687G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-99313295-G-A
• chr3-99313295-G-C
• chr3-99313295-G-T

Variant summary

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

The ENST00000474798.2(LINC00973):​n.1119-2687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,146 control chromosomes in the GnomAD database, including 62,911 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 (62911 hom., cov: 32)
• Consequence: LINC00973 ENST00000474798.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.960
• Publications: 2 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=-0.94).
• 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: ENST00000474798.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00973	ENST00000474798.2	TSL:5	n.1119-2687G>A		intron	N/A
	LINC00973	ENST00000749131.1		n.396-2687G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137403 AN: 152028 Hom.: 62891 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.904 AC: 137473 AN: 152146 Hom.: 62911 Cov.: 32 AF XY: 0.900 AC XY: 66906 AN XY: 74374

African (AFR) AF: 0.755 AC: 31325 AN: 41478

American (AMR) AF: 0.905 AC: 13808 AN: 15250

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

East Asian (EAS) AF: 0.855 AC: 4419 AN: 5170

South Asian (SAS) AF: 0.859 AC: 4150 AN: 4830

European-Finnish (FIN) AF: 0.934 AC: 9910 AN: 10610

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

European-Non Finnish (NFE) AF: 0.990 AC: 67329 AN: 68022

Other (OTH) AF: 0.930 AC: 1960 AN: 2108

Alfa AF: 0.935 Hom.: 8829

Bravo AF: 0.895

Asia WGS AF: 0.865 AC: 3011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.54
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs1383840; hg19: chr3-99032139;