NM_182532.3:c.15+1300G>C

Variant names:

• chr1-54982380-G-C
• rs2433675
• NM_182532.3:c.15+1300G>C

Variant summary

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

The NM_182532.3(TMEM61):​c.15+1300G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 151,966 control chromosomes in the GnomAD database, including 41,535 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 0.73 (41535 hom., cov: 30)
• Consequence: TMEM61 NM_182532.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 2 publications found

Genes affected

TMEM61 (HGNC:27296): (transmembrane protein 61) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000233271 (HGNC:):

DHCR24-DT (HGNC:53969): (DHCR24 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182532.3. 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
	TMEM61	NM_182532.3	MANE Select	c.15+1300G>C		intron	N/A	NP_872338.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM61	ENST00000371268.4	TSL:1 MANE Select	c.15+1300G>C		intron	N/A	ENSP00000360315.3
	TMEM61	ENST00000715913.1		c.15+1300G>C		intron	N/A	ENSP00000520542.1
	TMEM61	ENST00000715514.1		c.1-3717G>C		intron	N/A	ENSP00000520459.1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111575 AN: 151848 Hom.: 41513 Cov.: 30

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.735 AC: 111653 AN: 151966 Hom.: 41535 Cov.: 30 AF XY: 0.731 AC XY: 54320 AN XY: 74298

African (AFR) AF: 0.653 AC: 27050 AN: 41420

American (AMR) AF: 0.744 AC: 11357 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2576 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2423 AN: 5152

South Asian (SAS) AF: 0.706 AC: 3397 AN: 4812

European-Finnish (FIN) AF: 0.766 AC: 8095 AN: 10564

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54320 AN: 67964

Other (OTH) AF: 0.732 AC: 1546 AN: 2112

Alfa AF: 0.770 Hom.: 5670

Bravo AF: 0.727

Asia WGS AF: 0.607 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.67
PhyloP100		-3.0
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: rs2433675; hg19: chr1-55448053;