rs9290003

Variant names:

• chr3-100188149-T-C
• rs9290003
• ENST00000489487.2:n.343-1792T>C

Variant summary

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

The ENST00000489487.2(TMEM30CP):​n.343-1792T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,058 control chromosomes in the GnomAD database, including 19,001 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 0.50 (19001 hom., cov: 32)
• Consequence: TMEM30CP ENST00000489487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 4 publications found

Genes affected

TMEM30CP (HGNC:):

TMEM30CP (HGNC:30443): (transmembrane protein 30C, pseudogene) Predicted to be involved in phospholipid translocation. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM30CP	NR_028357.1	n.56-1792T>C		intron_variant	Intron 1 of 2
TMEM30CP	NR_028358.1	n.56-1792T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM30CP	ENST00000489487.2	n.343-1792T>C		intron_variant	Intron 2 of 3	1
TMEM30CP	ENST00000476804.2	n.56-1792T>C		intron_variant	Intron 1 of 1	2
TMEM30CP	ENST00000637814.1	n.193-1792T>C		intron_variant	Intron 1 of 6	6

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75305 AN: 151940 Hom.: 18970 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.496 AC: 75388 AN: 152058 Hom.: 19001 Cov.: 32 AF XY: 0.500 AC XY: 37155 AN XY: 74316

African (AFR) AF: 0.578 AC: 23962 AN: 41466

American (AMR) AF: 0.465 AC: 7104 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2402 AN: 5172

South Asian (SAS) AF: 0.543 AC: 2616 AN: 4822

European-Finnish (FIN) AF: 0.512 AC: 5407 AN: 10554

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31052 AN: 67970

Other (OTH) AF: 0.463 AC: 979 AN: 2114

Alfa AF: 0.462 Hom.: 62047

Bravo AF: 0.491

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.37
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9290003; hg19: chr3-99906993;