rs1474827

Variant names:

• chr6-134523180-T-A
• rs1474827
• ENST00000718375.1:n.109+152A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-134523180-T-A
• chr6-134523180-T-C
• chr6-134523180-T-G

Variant summary

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

The ENST00000718375.1(CT69):​n.109+152A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,126 control chromosomes in the GnomAD database, including 41,450 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 0.72 (41450 hom., cov: 32)
• Consequence: CT69 ENST00000718375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 1 publications found

Genes affected

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

ENSG00000293692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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
CT69	ENST00000718375.1	n.109+152A>T		intron_variant	Intron 1 of 4
CT69	ENST00000718379.1	n.214+152A>T		intron_variant	Intron 1 of 2
CT69	ENST00000718380.1	n.650+152A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109088 AN: 152008 Hom.: 41427 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.718 AC: 109154 AN: 152126 Hom.: 41450 Cov.: 32 AF XY: 0.723 AC XY: 53737 AN XY: 74374

African (AFR) AF: 0.444 AC: 18392 AN: 41436

American (AMR) AF: 0.832 AC: 12735 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2664 AN: 3468

East Asian (EAS) AF: 0.952 AC: 4933 AN: 5182

South Asian (SAS) AF: 0.843 AC: 4072 AN: 4828

European-Finnish (FIN) AF: 0.806 AC: 8534 AN: 10592

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55388 AN: 68002

Other (OTH) AF: 0.724 AC: 1528 AN: 2110

Alfa AF: 0.753 Hom.: 5521

Bravo AF: 0.709

Asia WGS AF: 0.871 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1474827; hg19: chr6-134844318; COSMIC: COSV69766767;