rs759293030

Variant names:

• chrX-128051939-T-A
• rs759293030
• NM_138289.4:c.268A>T

Your query was ambiguous. Multiple possible variants found:

• chrX-128051939-T-A
• chrX-128051939-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_138289.4(ACTRT1):​c.268A>T​(p.Lys90*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,098,126 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.000011 (0 hom. 2 hem.)
• Consequence: ACTRT1 NM_138289.4 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.929
• Publications: 0 publications found

Genes affected

ACTRT1 (HGNC:24027): (actin related protein T1) This gene encodes a protein related to the cytoskeletal protein beta-actin. This protein is a major component of the calyx in the perinuclear theca of mammalian sperm heads, and it therefore likely functions in spermatid formation. This gene is intronless and is similar to a related gene located on chromosome 1. A related pseudogene has also been identified approximately 75 kb downstream of this gene on chromosome X. [provided by RefSeq, May 2010]

ENSG00000225689 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Hemizygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTRT1	NM_138289.4	c.268A>T	p.Lys90*	stop_gained	Exon 1 of 1	ENST00000371124.5	NP_612146.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACTRT1	ENST00000371124.5	c.268A>T	p.Lys90*	stop_gained	Exon 1 of 1	6	NM_138289.4	ENSP00000360165.3
ENSG00000225689	ENST00000660383.1	n.1329-24586A>T		intron_variant	Intron 10 of 10

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 0.0000109 AC: 12 AN: 1098126 Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 2 AN XY: 363480

African (AFR) AF: 0.00 AC: 0 AN: 26403

American (AMR) AF: 0.00 AC: 0 AN: 35203

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19385

East Asian (EAS) AF: 0.00 AC: 0 AN: 30133

South Asian (SAS) AF: 0.00 AC: 0 AN: 54122

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40531

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4135

European-Non Finnish (NFE) AF: 0.0000142 AC: 12 AN: 842123

Other (OTH) AF: 0.00 AC: 0 AN: 46091

GnomAD4 genome Cov.: 22

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000346 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.29	D
BayesDel_noAF	Pathogenic	0.17
CADD	Pathogenic	31
DANN	Benign	0.97
FATHMM_MKL	Benign	0.52	D
PhyloP100		0.93
Vest4		0.037
GERP RS		0.12
PromoterAI		-0.0041	Neutral
Mutation Taster		=161/39	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs759293030; hg19: chrX-127185918;