rs4841072

Variant names:

• chr8-8933743-C-A
• rs4841072
• ENST00000603391.1:n.264G>T

Variant summary

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

The ENST00000603391.1(ENSG00000270966):​n.264G>T 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 0.584 in 1,312,058 control chromosomes in the GnomAD database, including 231,862 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 0.57 (25896 hom., cov: 31)
  • Exomes 𝑓: 0.59 (205966 hom.)
• Consequence: ENSG00000270966 ENST00000603391.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 4 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603391.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000270966	ENST00000603391.1	TSL:6	n.264G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000293372	ENST00000520582.2	TSL:3	n.254-110C>A		intron	N/A
	ENSG00000293372	ENST00000753008.1		n.368-110C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86513 AN: 151770 Hom.: 25854 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 0.586 AC: 679479 AN: 1160170 Hom.: 205966 Cov.: 18 AF XY: 0.580 AC XY: 342966 AN XY: 591060

African (AFR) AF: 0.747 AC: 21499 AN: 28766

American (AMR) AF: 0.284 AC: 12484 AN: 43904

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 15868 AN: 24392

East Asian (EAS) AF: 0.227 AC: 8493 AN: 37470

South Asian (SAS) AF: 0.481 AC: 38153 AN: 79332

European-Finnish (FIN) AF: 0.546 AC: 28396 AN: 52010

Middle Eastern (MID) AF: 0.630 AC: 2243 AN: 3560

European-Non Finnish (NFE) AF: 0.622 AC: 522955 AN: 840764

Other (OTH) AF: 0.588 AC: 29388 AN: 49972

GnomAD4 genome AF: 0.570 AC: 86602 AN: 151888 Hom.: 25896 Cov.: 31 AF XY: 0.559 AC XY: 41485 AN XY: 74202

African (AFR) AF: 0.705 AC: 29202 AN: 41416

American (AMR) AF: 0.396 AC: 6039 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2257 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1051 AN: 5164

South Asian (SAS) AF: 0.463 AC: 2232 AN: 4816

European-Finnish (FIN) AF: 0.519 AC: 5455 AN: 10514

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.567 AC: 38517 AN: 67932

Other (OTH) AF: 0.584 AC: 1232 AN: 2108

Alfa AF: 0.595 Hom.: 3423

Bravo AF: 0.562

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.49
DANN	Benign	0.44
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4841072; hg19: chr8-8791253;