rs970500

Variant names:

• chr15-38189912-A-C
• rs970500
• ENST00000561320.5:n.222+34339T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561320.5(LINC02895):​n.222+34339T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.948 in 152,152 control chromosomes in the GnomAD database, including 68,767 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 0.95 (68767 hom., cov: 30)
• Consequence: LINC02895 ENST00000561320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

Genes affected

LINC02895 (HGNC:55422): (long intergenic non-protein coding RNA 2895)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 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
LINC02895	ENST00000561320.5	n.222+34339T>G		intron_variant	Intron 2 of 3	1
LINC02895	ENST00000561161.2	n.254+34339T>G		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.948 AC: 144091 AN: 152034 Hom.: 68714 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.987

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.956

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

GnomAD4 genome AF: 0.948 AC: 144202 AN: 152152 Hom.: 68767 Cov.: 30 AF XY: 0.949 AC XY: 70609 AN XY: 74390

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.979

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.956

Alfa AF: 0.967 Hom.: 8861

Bravo AF: 0.942

Asia WGS AF: 0.981 AC: 3412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	9.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs970500; hg19: chr15-38482113;