rs7161307

Variant names:

• chr14-98141346-C-T
• rs7161307
• ENST00000555776.1:n.122-60821G>A

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-60821G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,956 control chromosomes in the GnomAD database, including 2,104 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 0.15 (2104 hom., cov: 32)
• Consequence: ENSG00000259097 ENST00000555776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 3 publications found

Genes affected

ENSG00000259097 (HGNC:):

LINC02295 (HGNC:53211): (long intergenic non-protein coding RNA 2295)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02295	NR_184268.1	n.529+2036C>T		intron_variant	Intron 2 of 2
LOC105370655	XR_001750876.2	n.95+24724G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259097	ENST00000555776.1	n.122-60821G>A		intron_variant	Intron 1 of 2	4
LINC02295	ENST00000684820.2	n.529+2036C>T		intron_variant	Intron 2 of 2
LINC02295	ENST00000691452.2	n.422+5149C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22552 AN: 151838 Hom.: 2105 Cov.: 32

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.148 AC: 22553 AN: 151956 Hom.: 2104 Cov.: 32 AF XY: 0.143 AC XY: 10629 AN XY: 74244

African (AFR) AF: 0.0744 AC: 3086 AN: 41458

American (AMR) AF: 0.144 AC: 2193 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5166

South Asian (SAS) AF: 0.0768 AC: 369 AN: 4806

European-Finnish (FIN) AF: 0.140 AC: 1473 AN: 10542

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14143 AN: 67938

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.168 Hom.: 328

Bravo AF: 0.147

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.68
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs7161307; hg19: chr14-98607683;