rs10193430

Variant names:

• chr2-103970893-T-A
• rs10193430
• ENST00000537492.5:n.137-82611T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-103970893-T-A
• chr2-103970893-T-G

Variant summary

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

The ENST00000537492.5(LINC01965):​n.137-82611T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,052 control chromosomes in the GnomAD database, including 2,654 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 0.18 (2654 hom., cov: 32)
• Consequence: LINC01965 ENST00000537492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 2 publications found

Genes affected

LINC01965 (HGNC:52790): (long intergenic non-protein coding RNA 1965)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537492.5. 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
	LINC01965	ENST00000537492.5	TSL:4	n.137-82611T>A		intron	N/A
	LINC01965	ENST00000544869.5	TSL:4	n.116-82611T>A		intron	N/A
	LINC01965	ENST00000688553.2		n.294-82611T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26954 AN: 151934 Hom.: 2649 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.177 AC: 26974 AN: 152052 Hom.: 2654 Cov.: 32 AF XY: 0.174 AC XY: 12939 AN XY: 74342

African (AFR) AF: 0.259 AC: 10741 AN: 41444

American (AMR) AF: 0.0978 AC: 1494 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3466

East Asian (EAS) AF: 0.245 AC: 1262 AN: 5156

South Asian (SAS) AF: 0.151 AC: 729 AN: 4820

European-Finnish (FIN) AF: 0.0976 AC: 1034 AN: 10594

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10587 AN: 67976

Other (OTH) AF: 0.149 AC: 316 AN: 2116

Alfa AF: 0.172 Hom.: 298

Bravo AF: 0.181

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.33
DANN	Benign	0.79
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10193430; hg19: chr2-104587351;