rs9290003

Positions:

• chr3-100188149-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_028357.1(TMEM30CP):​n.56-1792T>C variant causes a intron, non coding transcript 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 NR_028357.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TMEM30CP	NR_028357.1	n.56-1792T>C		intron_variant, non_coding_transcript_variant
TMEM30CP	NR_028358.1	n.56-1792T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM30CP	ENST00000489487.1	n.56-1792T>C		intron_variant, non_coding_transcript_variant		1
TMEM30CP	ENST00000637814.1	n.193-1792T>C		intron_variant, non_coding_transcript_variant
	ENST00000654821.1	n.196-36199A>G		intron_variant, non_coding_transcript_variant
TMEM30CP	ENST00000476804.2	n.56-1792T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.463

Alfa AF: 0.452 Hom.: 25773

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290003; hg19: chr3-99906993;