dbSNP rs5945572: :null (chrX-51486831-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is The variant received -4 classification points (ACMG Germline Pathogenicity v2019). BP4_Strong

The variant X-51486831-A-G has been identified. No reliable population frequency data is available for this variant in the gnomAD database. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.68 ( 18424 hom., 22265 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

90 publications found

Variant links:

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Classification according to ACMG Germline Pathogenicity v2019

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

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

Variant Effect in Transcripts

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.684	AC:75450	Hom:18422	AN:110377	Cov:23
GnomAD4 genome Warning	AF: 0.684	AC:75506	Hom:18424	AN:110434	Cov:23
TOPMed (Bravo)	AF: 0.705	AC:186582	Hom:78474	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.666	AC:244995	Hom:101667	AN:367736	Cov:
Local & regional cohorts 7 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.713	AC:1366	Hom:378	AN:1916	Cov:
Denmark Genome	AF: 0.738	AC:172	Hom:	AN:233	Cov:
Korea4K (4,157 Koreans)	AF: 0.917	AC:4777	Hom:	AN:5210	Cov:
Qatari Genome	AF: 0.670	AC:59	Hom:	AN:88	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.911	AC:93031	Hom:33785	AN:102065	Cov:
Turkish Variome	AF: 0.678	AC:1032	Hom:448	AN:1522	Cov:
UK10K	AF: 0.638	AC:4209	Hom:	AN:6597	Cov:

Showing 11 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	0.091
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.046
DANN	Benign	0.43
GPN-Star LLR	N/A	-0.34
GPN-Star score	N/A	0.34
PhyloP100	Benign	-1.8

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

Publications

Other links and lift over