rs10512897

Variant names:

• chr5-6964215-G-A
• rs10512897
• ENST00000512838.2:n.69+30477G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-6964215-G-A
• chr5-6964215-G-T

Variant summary

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

The ENST00000512838.2(LINC02196):​n.69+30477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,070 control chromosomes in the GnomAD database, including 10,038 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 0.33 (10038 hom., cov: 32)
• Consequence: LINC02196 ENST00000512838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 1 publications found

Genes affected

LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512838.2. 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
	LINC02196	ENST00000512838.2	TSL:4	n.69+30477G>A		intron	N/A
	LINC02196	ENST00000648809.1		n.362+40287G>A		intron	N/A
	LINC02196	ENST00000715905.1		n.277+40287G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49692 AN: 151952 Hom.: 10041 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.327 AC: 49696 AN: 152070 Hom.: 10038 Cov.: 32 AF XY: 0.325 AC XY: 24183 AN XY: 74306

African (AFR) AF: 0.127 AC: 5280 AN: 41502

American (AMR) AF: 0.302 AC: 4613 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1939 AN: 3470

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5180

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4820

European-Finnish (FIN) AF: 0.472 AC: 4977 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30211 AN: 67964

Other (OTH) AF: 0.344 AC: 726 AN: 2112

Alfa AF: 0.267 Hom.: 990

Bravo AF: 0.302

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		0.017

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: rs10512897;

hg19: chr5-6964328;