9-27608587-G-C

Variant names:

• chr9-27608587-G-C
• rs634157
• ENST00000400348.3:n.2159C>G

Variant summary

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

The ENST00000400348.3(CTAGE12P):​n.2159C>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 0.278 in 1,595,406 control chromosomes in the GnomAD database, including 63,792 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 0.26 (5345 hom., cov: 32)
  • Exomes 𝑓: 0.28 (58447 hom.)
• Consequence: CTAGE12P ENST00000400348.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517
• Publications: 2 publications found

Genes affected

CTAGE12P (HGNC:37297): (CTAGE family member 12, pseudogene)

ENSG00000307594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTAGE12P		n.27608587G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTAGE12P	ENST00000400348.3	n.2159C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000307594	ENST00000827310.1	n.697-22201C>G		intron_variant	Intron 3 of 3
ENSG00000307594	ENST00000827311.1	n.389-22201C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38799 AN: 151924 Hom.: 5345 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.261

GnomAD4 exome AF: 0.280 AC: 404568 AN: 1443364 Hom.: 58447 Cov.: 35 AF XY: 0.283 AC XY: 203551 AN XY: 718264

African (AFR) AF: 0.146 AC: 4843 AN: 33088

American (AMR) AF: 0.251 AC: 11145 AN: 44414

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 6432 AN: 25896

East Asian (EAS) AF: 0.434 AC: 17100 AN: 39434

South Asian (SAS) AF: 0.340 AC: 29200 AN: 85882

European-Finnish (FIN) AF: 0.310 AC: 16220 AN: 52372

Middle Eastern (MID) AF: 0.280 AC: 1598 AN: 5708

European-Non Finnish (NFE) AF: 0.275 AC: 301664 AN: 1097112

Other (OTH) AF: 0.275 AC: 16366 AN: 59458

GnomAD4 genome AF: 0.255 AC: 38802 AN: 152042 Hom.: 5345 Cov.: 32 AF XY: 0.260 AC XY: 19307 AN XY: 74302

African (AFR) AF: 0.159 AC: 6583 AN: 41476

American (AMR) AF: 0.232 AC: 3545 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3472

East Asian (EAS) AF: 0.444 AC: 2289 AN: 5150

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3298 AN: 10556

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19515 AN: 67978

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.159 Hom.: 348

Bravo AF: 0.244

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs634157; hg19: chr9-27608585;