rs7079573

Variant names:

• chr10-44904958-G-A
• rs7079573
• ENST00000436877.2:n.532+1927C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-44904958-G-A
• chr10-44904958-G-C
• chr10-44904958-G-T

Variant summary

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

The ENST00000436877.2(ENSG00000234504):​n.532+1927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,632 control chromosomes in the GnomAD database, including 23,552 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 0.55 (23552 hom., cov: 32)
• Consequence: ENSG00000234504 ENST00000436877.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 2 publications found

Genes affected

ENSG00000234504 (HGNC:):

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=-0.92).
• 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 rank	MANE	Protein	UniProt
TMEM72-AS1	NR_033842.1	n.244+18123C>T		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234504	ENST00000436877.2	n.532+1927C>T		intron_variant	Intron 2 of 2	5
TMEM72-AS1	ENST00000450287.2	n.244+18123C>T		intron_variant	Intron 2 of 7	2
TMEM72-AS1	ENST00000656140.1	n.177+18123C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84069 AN: 151518 Hom.: 23528 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.555 AC: 84141 AN: 151632 Hom.: 23552 Cov.: 32 AF XY: 0.550 AC XY: 40744 AN XY: 74088

African (AFR) AF: 0.550 AC: 22731 AN: 41306

American (AMR) AF: 0.549 AC: 8373 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1963 AN: 3464

East Asian (EAS) AF: 0.357 AC: 1836 AN: 5144

South Asian (SAS) AF: 0.559 AC: 2688 AN: 4810

European-Finnish (FIN) AF: 0.505 AC: 5313 AN: 10516

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39291 AN: 67840

Other (OTH) AF: 0.543 AC: 1136 AN: 2092

Alfa AF: 0.453 Hom.: 1333

Bravo AF: 0.559

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.21
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7079573; hg19: chr10-45400406;