rs41269315

Variant names:

• chr6-75253237-G-A
• rs41269315
• NM_018247.4:c.*2865C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-75253237-G-A
• chr6-75253237-G-C

Variant summary

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

The NM_018247.4(TMEM30A):​c.*2865C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 152,140 control chromosomes in the GnomAD database, including 234 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 0.045 (234 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: TMEM30A NM_018247.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 5 publications found

Genes affected

TMEM30A (HGNC:16667): (transmembrane protein 30A) Enables aminophospholipid flippase activity. Involved in several processes, including phospholipid transport; positive regulation of transport; and xenobiotic transmembrane transport. Located in endoplasmic reticulum and plasma membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000297216 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM30A	NM_018247.4	c.*2865C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000230461.11	NP_060717.1
TMEM30A	NM_001143958.2	c.*2865C>T		3_prime_UTR_variant	Exon 6 of 6		NP_001137430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM30A	ENST00000230461.11	c.*2865C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_018247.4	ENSP00000230461.6

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6781 AN: 152014 Hom.: 234 Cov.: 32

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00518

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0422

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 1 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0446 AC: 6781 AN: 152132 Hom.: 234 Cov.: 32 AF XY: 0.0458 AC XY: 3403 AN XY: 74376

African (AFR) AF: 0.0105 AC: 438 AN: 41544

American (AMR) AF: 0.0420 AC: 642 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00540 AC: 26 AN: 4818

European-Finnish (FIN) AF: 0.126 AC: 1331 AN: 10568

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0599 AC: 4072 AN: 67960

Other (OTH) AF: 0.0417 AC: 88 AN: 2108

Alfa AF: 0.0496 Hom.: 95

Bravo AF: 0.0371

Asia WGS AF: 0.00635 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs41269315; hg19: chr6-75962953;