8-8933998-C-T

Variant names:

• chr8-8933998-C-T
• rs17154962
• ENST00000603391.1:n.9G>A

Variant summary

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

The ENST00000603391.1(ENSG00000270966):​n.9G>A 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 0.11 in 1,581,632 control chromosomes in the GnomAD database, including 12,903 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 0.17 (3372 hom., cov: 32)
  • Exomes 𝑓: 0.10 (9531 hom.)
• Consequence: ENSG00000270966 ENST00000603391.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 3 publications found

Genes affected

ENSG00000270966 (HGNC:):

MRPS18CP2 (HGNC:29743):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPS18CP2		n.8933998C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270966	ENST00000603391.1	n.9G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293372	ENST00000753030.1	n.223C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000293372	ENST00000520582.2	n.357+42C>T		intron_variant	Intron 3 of 7	3

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26003 AN: 151958 Hom.: 3369 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.103 AC: 147575 AN: 1429556 Hom.: 9531 Cov.: 28 AF XY: 0.103 AC XY: 73418 AN XY: 712712

African (AFR) AF: 0.375 AC: 12139 AN: 32328

American (AMR) AF: 0.0664 AC: 2954 AN: 44496

Ashkenazi Jewish (ASJ) AF: 0.0721 AC: 1866 AN: 25890

East Asian (EAS) AF: 0.144 AC: 5660 AN: 39416

South Asian (SAS) AF: 0.122 AC: 10443 AN: 85418

European-Finnish (FIN) AF: 0.131 AC: 6930 AN: 53084

Middle Eastern (MID) AF: 0.142 AC: 577 AN: 4062

European-Non Finnish (NFE) AF: 0.0921 AC: 100005 AN: 1085888

Other (OTH) AF: 0.119 AC: 7001 AN: 58974

GnomAD4 genome AF: 0.171 AC: 26036 AN: 152076 Hom.: 3372 Cov.: 32 AF XY: 0.173 AC XY: 12858 AN XY: 74360

African (AFR) AF: 0.364 AC: 15075 AN: 41426

American (AMR) AF: 0.0965 AC: 1474 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3470

East Asian (EAS) AF: 0.116 AC: 599 AN: 5168

South Asian (SAS) AF: 0.119 AC: 574 AN: 4822

European-Finnish (FIN) AF: 0.129 AC: 1368 AN: 10586

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0923 AC: 6280 AN: 68008

Other (OTH) AF: 0.152 AC: 322 AN: 2114

Alfa AF: 0.132 Hom.: 341

Bravo AF: 0.178

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.68
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs17154962; hg19: chr8-8791508;