rs2295199

Variant names:

• chr6-134454367-C-A
• rs2295199
• ENST00000417483.5:n.316+86G>T

Variant summary

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

The ENST00000431422.3(LINC01010):​n.621-10374C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,110 control chromosomes in the GnomAD database, including 13,020 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 0.40 (13019 hom., cov: 32)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 5 publications found

Genes affected

CT69 (HGNC:37196): (cancer/testis associated transcript 69)

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431422.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01010	NR_038216.1		n.167-10374C>A		intron	N/A
	LINC01010	NR_038217.1		n.167-10374C>A		intron	N/A
	LINC01010	NR_038218.1		n.133-10374C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CT69	ENST00000417483.5	TSL:3	n.316+86G>T		intron	N/A
	CT69	ENST00000422736.2	TSL:3	n.261+86G>T		intron	N/A
	LINC01010	ENST00000431422.3	TSL:2	n.621-10374C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60305 AN: 151976 Hom.: 13013 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.385

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 1 AF XY: 0.286 AC XY: 4 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 4 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.397 AC: 60311 AN: 152094 Hom.: 13019 Cov.: 32 AF XY: 0.399 AC XY: 29684 AN XY: 74346

African (AFR) AF: 0.229 AC: 9483 AN: 41496

American (AMR) AF: 0.369 AC: 5632 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1646 AN: 5158

South Asian (SAS) AF: 0.479 AC: 2308 AN: 4820

European-Finnish (FIN) AF: 0.518 AC: 5484 AN: 10580

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33040 AN: 67978

Other (OTH) AF: 0.384 AC: 811 AN: 2110

Alfa AF: 0.452 Hom.: 51473

Bravo AF: 0.377

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.10
DANN	Benign	0.76
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2295199; hg19: chr6-134775505;