rs1408814

chr10-44903640-A-G

Variant summary

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

The NR_033842.1(TMEM72-AS1):n.244+19441T>C 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 0.558 in 152,060 control chromosomes in the GnomAD database, including 23,946 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 0.56 (23946 hom., cov: 32)
• Consequence: TMEM72-AS1 NR_033842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

(HGNC:):

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM72-AS1	NR_033842.1	n.244+19441T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000436877.2	n.533-3115T>C		intron_variant, non_coding_transcript_variant		5
TMEM72-AS1	ENST00000669460.1	n.265-18340T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84778 AN: 151942 Hom.: 23922 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.558 AC: 84853 AN: 152060 Hom.: 23946 Cov.: 32 AF XY: 0.553 AC XY: 41109 AN XY: 74320

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.549

Alfa AF: 0.569 Hom.: 41648

Bravo AF: 0.562

Asia WGS AF: 0.486 AC: 1690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.9
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: rs1408814; hg19: chr10-45399088;