rs17546037

Variant names:

• chr5-7217290-A-G
• rs17546037
• ENST00000651243.2:n.491-495A>G

Variant summary

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

The ENST00000651243.2(LINC02196):​n.491-495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,264 control chromosomes in the GnomAD database, including 854 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 0.10 (854 hom., cov: 32)
• Consequence: LINC02196 ENST00000651243.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 2 publications found

Genes affected

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

ENSG00000308577 (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 = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02196	ENST00000651243.2	n.491-495A>G		intron_variant	Intron 4 of 4
ENSG00000308577	ENST00000835169.1	n.123+33349T>C		intron_variant	Intron 1 of 2
ENSG00000308577	ENST00000835170.1	n.96+33349T>C		intron_variant	Intron 1 of 2
ENSG00000308577	ENST00000835171.1	n.94+33349T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15249 AN: 152146 Hom.: 856 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.100 AC: 15260 AN: 152264 Hom.: 854 Cov.: 32 AF XY: 0.0992 AC XY: 7383 AN XY: 74442

African (AFR) AF: 0.0944 AC: 3922 AN: 41564

American (AMR) AF: 0.0575 AC: 879 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3472

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5180

South Asian (SAS) AF: 0.0817 AC: 394 AN: 4824

European-Finnish (FIN) AF: 0.134 AC: 1423 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7706 AN: 68016

Other (OTH) AF: 0.0938 AC: 198 AN: 2110

Alfa AF: 0.112 Hom.: 171

Bravo AF: 0.0940

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.22
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs17546037; hg19: chr5-7217403;