rs2270162

Positions:

• chr7-69596980-C-G
• chr7-69596980-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_108105.2(CT66):​n.391+254G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 152,312 control chromosomes in the GnomAD database, including 106 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 0.028 (106 hom., cov: 33)
• Consequence: CT66 NR_108105.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

CT66 (HGNC:54198): (cancer/testis associated transcript 66)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CT66	NR_108105.2	n.391+254G>C		intron_variant, non_coding_transcript_variant
CT66	NR_148926.1	n.391+254G>C		intron_variant, non_coding_transcript_variant
CT66	NR_148927.1	n.578+67G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CT66	ENST00000669908.1	n.260+254G>C		intron_variant, non_coding_transcript_variant
CT66	ENST00000436600.2	n.215+254G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0281 AC: 4284 AN: 152194 Hom.: 107 Cov.: 33

Gnomad AFR AF: 0.00560

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0281 AC: 4278 AN: 152312 Hom.: 106 Cov.: 33 AF XY: 0.0299 AC XY: 2224 AN XY: 74476

Gnomad4 AFR AF: 0.00558

Gnomad4 AMR AF: 0.0146

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0243

Gnomad4 FIN AF: 0.0541

Gnomad4 NFE AF: 0.0348

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0188 Hom.: 9

Bravo AF: 0.0243

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.94
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2270162; hg19: chr7-69061966;