1-205275825-G-A

Variant names:

• chr1-205275825-G-A
• rs1172130
• ENST00000648708.1:n.114-2203G>A

Variant summary

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

The ENST00000648708.1(TMCC2):​n.114-2203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,058 control chromosomes in the GnomAD database, including 7,607 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 0.30 (7607 hom., cov: 32)
• Consequence: TMCC2 ENST00000648708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 30 publications found

Genes affected

TMCC2 (HGNC:24239): (transmembrane and coiled-coil domain family 2) Involved in amyloid precursor protein metabolic process. Located in endoplasmic reticulum. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648708.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMCC2	ENST00000648708.1		n.114-2203G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44974 AN: 151938 Hom.: 7606 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.296 AC: 44976 AN: 152058 Hom.: 7607 Cov.: 32 AF XY: 0.293 AC XY: 21781 AN XY: 74316

African (AFR) AF: 0.178 AC: 7383 AN: 41494

American (AMR) AF: 0.246 AC: 3757 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1123 AN: 3472

East Asian (EAS) AF: 0.111 AC: 572 AN: 5166

South Asian (SAS) AF: 0.143 AC: 687 AN: 4820

European-Finnish (FIN) AF: 0.439 AC: 4633 AN: 10546

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25889 AN: 67964

Other (OTH) AF: 0.295 AC: 622 AN: 2110

Alfa AF: 0.328 Hom.: 14653

Bravo AF: 0.275

Asia WGS AF: 0.125 AC: 439 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	0.34
DANN	Benign	0.34
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1172130; hg19: chr1-205244953;