rs2433675

chr1-54982380-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

TMEM61 (HGNC:27296): (transmembrane protein 61) Predicted to be integral component of 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM61	NM_182532.3	c.15+1300G>C		intron_variant		ENST00000371268.4
TMEM61	XM_005270586.5	c.-1+1712G>C		intron_variant
TMEM61	XM_011540911.3	c.15+1300G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM61	ENST00000371268.4	c.15+1300G>C		intron_variant		1	NM_182532.3	P1
	ENST00000436960.1	n.363-1365C>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.732

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.46
Dann	Benign	0.67

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: rs2433675; hg19: chr1-55448053;