rs1017783

Variant names:

• chr9-22920665-G-A
• rs1017783
• ENST00000640003.1:n.369-46346C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-22920665-G-A
• chr9-22920665-G-C
• chr9-22920665-G-T

Variant summary

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

The ENST00000764217.1(LINC03142):​n.119-46346C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 150,114 control chromosomes in the GnomAD database, including 8,583 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 0.31 (8583 hom., cov: 30)
• Consequence: LINC03142 ENST00000764217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 12 publications found

Genes affected

LINC03142 (HGNC:58153):

LOC105375990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764217.1. 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
	LINC03142	ENST00000640003.1	TSL:5	n.369-46346C>T		intron	N/A
	LINC03142	ENST00000764217.1		n.119-46346C>T		intron	N/A
	LINC03142	ENST00000764218.1		n.119-46346C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 46760 AN: 149998 Hom.: 8581 Cov.: 30

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.416

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.312 AC: 46766 AN: 150114 Hom.: 8583 Cov.: 30 AF XY: 0.317 AC XY: 23167 AN XY: 73196

African (AFR) AF: 0.117 AC: 4757 AN: 40648

American (AMR) AF: 0.421 AC: 6318 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1404 AN: 3452

East Asian (EAS) AF: 0.158 AC: 796 AN: 5044

South Asian (SAS) AF: 0.346 AC: 1640 AN: 4738

European-Finnish (FIN) AF: 0.455 AC: 4695 AN: 10330

Middle Eastern (MID) AF: 0.406 AC: 116 AN: 286

European-Non Finnish (NFE) AF: 0.386 AC: 26109 AN: 67632

Other (OTH) AF: 0.325 AC: 672 AN: 2070

Alfa AF: 0.354 Hom.: 7618

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.40
PhyloP100		-0.34

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: rs1017783;

hg19: chr9-22920664;