10-44890874-G-T

Position:

• chr10-44890874-G-T

Variant summary

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

The ENST00000450287.2(TMEM72-AS1):​n.244+32207C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,066 control chromosomes in the GnomAD database, including 22,651 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 0.54 (22651 hom., cov: 33)
• Consequence: TMEM72-AS1 ENST00000450287.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

Genes affected

TMEM72-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM72-AS1	NR_033842.1	n.244+32207C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM72-AS1	ENST00000450287.2	n.244+32207C>A		intron_variant		2
TMEM72-AS1	ENST00000656140.1	n.178-5574C>A		intron_variant
TMEM72-AS1	ENST00000657040.1	n.124-5574C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82517 AN: 151946 Hom.: 22633 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.543 AC: 82580 AN: 152066 Hom.: 22651 Cov.: 33 AF XY: 0.539 AC XY: 40065 AN XY: 74314

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.544

Alfa AF: 0.569 Hom.: 4902

Bravo AF: 0.546

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10900126; hg19: chr10-45386322;