10-119001997-A-G

Variant names:

• chr10-119001997-A-G
• rs555938
• ENST00000663084.1:n.264+23800T>C

Variant summary

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

The NR_186540.1(LINC03036):​n.291+23800T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,788 control chromosomes in the GnomAD database, including 29,488 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 0.62 (29488 hom., cov: 31)
• Consequence: LINC03036 NR_186540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 2 publications found

Genes affected

LINC03036 (HGNC:56220): (long intergenic non-protein coding RNA 3036)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186540.1. 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
	LINC03036	NR_186540.1		n.291+23800T>C		intron	N/A
	LINC03036	NR_186541.1		n.303+23788T>C		intron	N/A
	LINC03036	NR_186542.1		n.417-49T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03036	ENST00000663084.1		n.264+23800T>C		intron	N/A
	LINC03036	ENST00000762832.1		n.507-49T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94111 AN: 151670 Hom.: 29488 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.620 AC: 94137 AN: 151788 Hom.: 29488 Cov.: 31 AF XY: 0.618 AC XY: 45817 AN XY: 74164

African (AFR) AF: 0.530 AC: 21930 AN: 41396

American (AMR) AF: 0.605 AC: 9231 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2218 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3037 AN: 5154

South Asian (SAS) AF: 0.605 AC: 2912 AN: 4812

European-Finnish (FIN) AF: 0.664 AC: 6996 AN: 10532

Middle Eastern (MID) AF: 0.614 AC: 178 AN: 290

European-Non Finnish (NFE) AF: 0.674 AC: 45770 AN: 67882

Other (OTH) AF: 0.629 AC: 1324 AN: 2104

Alfa AF: 0.628 Hom.: 9979

Bravo AF: 0.614

Asia WGS AF: 0.594 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.49
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs555938; hg19: chr10-120761509;