rs970500

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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
LINC02895	ENST00000728143.1	n.248+34339T>G		intron_variant	Intron 2 of 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

African (AFR) AF: 0.827 AC: 34288 AN: 41452

American (AMR) AF: 0.979 AC: 14973 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3360 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5135 AN: 5176

South Asian (SAS) AF: 0.987 AC: 4744 AN: 4808

European-Finnish (FIN) AF: 1.00 AC: 10612 AN: 10612

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67870 AN: 68016

Other (OTH) AF: 0.956 AC: 2022 AN: 2114

Alfa AF: 0.962 Hom.: 9134

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs970500; hg19: chr15-38482113;