Genetic Variant ENSG00000291034:n.451-61723C>T (chrY-12303131-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000651802.1(ENSG00000291034):n.451-61723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.026 ( 0 hom., 871 hem., cov: 0)

Consequence

ENSG00000291034
ENST00000651802.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

1 publications found

Variant links:

Genes affected

ENSG00000291034 (HGNC:):

ENSG00000291034 links:

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new If you want to explore the variant's impact on the transcript ENST00000651802.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651802.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000291034	ENST00000651802.1		n.451-61723C>T		intron	N/A
	ENSG00000291034	ENST00000651835.1		n.320-45100C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0264

AC:

868

AN:

32902

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00512

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.0577

Gnomad ASJ

AF:

0.0798

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0306

Gnomad FIN

AF:

0.000297

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.0337

Gnomad OTH

AF:

0.0375

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

GnomAD4 genome

AF:

0.0264

AC:

871

AN:

32967

Hom.:

Cov.:

AF XY:

0.0264

AC XY:

871

AN XY:

32967

show subpopulations

African (AFR)

AF:

0.00509

AC:

AN:

8448

American (AMR)

AF:

0.0576

AC:

205

AN:

3559

Ashkenazi Jewish (ASJ)

AF:

0.0798

AC:

AN:

764

East Asian (EAS)

AF:

0.00

AC:

AN:

1237

South Asian (SAS)

AF:

0.0312

AC:

AN:

1410

European-Finnish (FIN)

AF:

0.000297

AC:

AN:

3364

Middle Eastern (MID)

AF:

0.206

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0338

AC:

455

AN:

13452

Other (OTH)

AF:

0.0373

AC:

AN:

456

Age Distribution

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

(source)

PhyloP100

0.064

Splicing

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

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over