Y-21548157-G-T

Variant names:

• chrY-21548157-G-T
• NM_005058.4:c.1097G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005058.4(RBMY1A1):​c.1097G>T​(p.Gly366Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: RBMY1A1 NM_005058.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.49

Genes affected

RBMY1A1 (HGNC:9912): (RNA binding motif protein Y-linked family 1 member A1) This gene encodes a protein containing an RNA-binding motif in the N-terminus and four SRGY (serine, arginine, glycine, tyrosine) boxes in the C-terminus. This protein is thought to function as a splicing regulator during spermatogenesis. Multiple closely related paralogs of this gene are found in a gene cluster in the AZFb azoospermia factor region of chromosome Y. Most of these related copies are thought to be pseudogenes, though several likely encode functional proteins. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBMY1A1	NM_005058.4	c.1097G>T	p.Gly366Val	missense_variant	Exon 10 of 12	ENST00000382707.6	NP_005049.1
RBMY1A1	NM_001320945.2	c.677G>T	p.Gly226Val	missense_variant	Exon 9 of 11		NP_001307874.1
RBMY1A1	XM_011531437.3	c.1097G>T	p.Gly366Val	missense_variant	Exon 10 of 12		XP_011529739.1
RBMY1A1	NM_001320944.2	c.993-93G>T		intron_variant	Intron 9 of 10		NP_001307873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBMY1A1	ENST00000382707.6	c.1097G>T	p.Gly366Val	missense_variant	Exon 10 of 12	1	NM_005058.4	ENSP00000372154.2
RBMY1A1	ENST00000361046.4	n.*673G>T		non_coding_transcript_exon_variant	Exon 9 of 11	1		ENSP00000354329.4
RBMY1A1	ENST00000361046.4	n.*673G>T		3_prime_UTR_variant	Exon 9 of 11	1		ENSP00000354329.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Jan 20, 2023

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.95
DEOGEN2	Benign	0.11	T;T
FATHMM_MKL	Benign	0.61	D
LIST_S2	Benign	0.74	T;.
M_CAP	Pathogenic	0.92	D
MetaRNN	Uncertain	0.59	D;D
MutationAssessor	Benign	0.34	N;N
PROVEAN	Uncertain	-4.3	.;D
Sift	Benign	0.14	.;T
Sift4G	Uncertain	0.038	D;D
Vest4		0.49
MVP		0.061
Varity_R		0.32
gMVP		0.0038

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrY-23710043;