rs12772980

Positions:

• chr10-44877775-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033842.1(TMEM72-AS1):​n.245-42456T>G variant causes a intron, non coding transcript 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 NR_033842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TMEM72-AS1	NR_033842.1	n.245-42456T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM72-AS1	ENST00000669460.1	n.357+7433T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0307

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.126

Alfa AF: 0.110 Hom.: 133

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12772980; hg19: chr10-45373223;