rs7911712

Positions:

• chr10-44824206-G-A

Variant summary

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

The ENST00000450287.2(TMEM72-AS1):​n.2042-918C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,092 control chromosomes in the GnomAD database, including 1,143 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 0.11 (1143 hom., cov: 33)
• Consequence: TMEM72-AS1 ENST00000450287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

Genes affected

TMEM72-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM72-AS1	NR_033842.1	n.2042-918C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM72-AS1	ENST00000450287.2	n.2042-918C>T		intron_variant		2
TMEM72-AS1	ENST00000657040.1	n.217-28665C>T		intron_variant
TMEM72-AS1	ENST00000659078.1	n.2343-918C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17439 AN: 151974 Hom.: 1143 Cov.: 33

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.115 AC: 17460 AN: 152092 Hom.: 1143 Cov.: 33 AF XY: 0.112 AC XY: 8357 AN XY: 74352

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.0996

Alfa AF: 0.136 Hom.: 3037

Bravo AF: 0.108

Asia WGS AF: 0.0350 AC: 122 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7911712; hg19: chr10-45319654;