rs2270162

Variant names:

• chr7-69596980-C-G
• rs2270162
• ENST00000779167.1:n.677C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000779167.1(ENSG00000301483):​n.677C>G variant causes a non coding transcript exon 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: ENSG00000301483 ENST00000779167.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 1 publications found

Genes affected

ENSG00000301483 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CT66	NR_108105.2	n.391+254G>C		intron_variant	Intron 1 of 1
CT66	NR_148926.1	n.391+254G>C		intron_variant	Intron 1 of 2
CT66	NR_148927.1	n.578+67G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301483	ENST00000779167.1	n.677C>G		non_coding_transcript_exon_variant	Exon 3 of 3
CT66	ENST00000779420.1	n.439G>C		non_coding_transcript_exon_variant	Exon 1 of 2
CT66	ENST00000436600.2	n.215+254G>C		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.00558 AC: 232 AN: 41576

American (AMR) AF: 0.0146 AC: 224 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3470

East Asian (EAS) AF: 0.130 AC: 673 AN: 5180

South Asian (SAS) AF: 0.0243 AC: 117 AN: 4818

European-Finnish (FIN) AF: 0.0541 AC: 574 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2366 AN: 68022

Other (OTH) AF: 0.0232 AC: 49 AN: 2116

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2270162; hg19: chr7-69061966;