rs12772980

Variant names:

• chr10-44877775-A-C
• rs12772980
• ENST00000717482.1:n.1042T>G

Variant summary

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

The ENST00000717482.1(TMEM72-AS1):​n.1042T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 152,304 control chromosomes in the GnomAD database, including 956 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 0.098 (956 hom., cov: 32)
• Consequence: TMEM72-AS1 ENST00000717482.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 0 publications found

Genes affected

TMEM72-AS1 (HGNC:27349): (TMEM72 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM72-AS1	NR_033842.1	n.245-42456T>G		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM72-AS1	ENST00000717482.1	n.1042T>G		non_coding_transcript_exon_variant	Exon 7 of 7
TMEM72-AS1	ENST00000813786.1	n.839T>G		non_coding_transcript_exon_variant	Exon 6 of 6
TMEM72-AS1	ENST00000813795.1	n.785T>G		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 14898 AN: 152184 Hom.: 954 Cov.: 32

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0865

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.0978 AC: 14896 AN: 152304 Hom.: 956 Cov.: 32 AF XY: 0.0944 AC XY: 7027 AN XY: 74478

African (AFR) AF: 0.0307 AC: 1278 AN: 41580

American (AMR) AF: 0.103 AC: 1579 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0867 AC: 419 AN: 4830

European-Finnish (FIN) AF: 0.0949 AC: 1007 AN: 10608

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9731 AN: 68008

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.106 Hom.: 134

Bravo AF: 0.0961

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.70
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12772980; hg19: chr10-45373223;