15-93953070-T-C

Variant names:

• chr15-93953070-T-C
• rs10438448
• ENST00000555364.7:n.219-16524T>C

Variant summary

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

The ENST00000555364.7(LINC02207):​n.219-16524T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,106 control chromosomes in the GnomAD database, including 4,193 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 0.22 (4193 hom., cov: 32)
• Consequence: LINC02207 ENST00000555364.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 2 publications found

Genes affected

LINC02207 (HGNC:53073): (long intergenic non-protein coding RNA 2207)

LINC01581 (HGNC:51415): (long intergenic non-protein coding RNA 1581)

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

LINC01580 (HGNC:51414): (long intergenic non-protein coding RNA 1580)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01581	NR_120320.1	n.2015-3849A>G		intron_variant	Intron 6 of 8
LINC01580	NR_120322.1	n.197-16524T>C		intron_variant	Intron 2 of 3
LINC01580	NR_120323.1	n.197-30716T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02207	ENST00000555364.7	n.219-16524T>C		intron_variant	Intron 2 of 3	1
LINC01581	ENST00000558874.1	n.2015-3849A>G		intron_variant	Intron 6 of 8	1
LINC02207	ENST00000555255.1	n.197-30716T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33727 AN: 151988 Hom.: 4196 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.222 AC: 33722 AN: 152106 Hom.: 4193 Cov.: 32 AF XY: 0.222 AC XY: 16504 AN XY: 74362

African (AFR) AF: 0.112 AC: 4652 AN: 41502

American (AMR) AF: 0.208 AC: 3176 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3470

East Asian (EAS) AF: 0.170 AC: 879 AN: 5182

South Asian (SAS) AF: 0.271 AC: 1308 AN: 4830

European-Finnish (FIN) AF: 0.267 AC: 2818 AN: 10554

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19292 AN: 67974

Other (OTH) AF: 0.210 AC: 444 AN: 2110

Alfa AF: 0.247 Hom.: 2861

Bravo AF: 0.207

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.50
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs10438448; hg19: chr15-94496299;