dbSNP rs2337080: ENSG00000309435:n.1037A>G (chrY-9903745-T-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000841136.1(ENSG00000309435):n.1037A>G variant causes a non coding transcript exon 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 0.0018 ( 0 hom., 47 hem., cov: 0)

Consequence

ENSG00000309435
ENST00000841136.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

Publications

2 publications found

Variant links:

COSMIC-nc: COSV100164344

Genes affected

ENSG00000309435 (HGNC:):

ENSG00000309435 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000841136.1, 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 -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BS2

High Hemizygotes in GnomAd4 at 47 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841136.1. 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

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000309435	ENST00000841136.1	n.1037A>G	non_coding_transcript_exon	Exon 7 of 7
ENSG00000309435	ENST00000841128.1	n.890+338A>G	intron	N/A
ENSG00000309435	ENST00000841129.1	n.732+338A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00175

AC:

AN:

26337

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00196

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00179

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000968

Gnomad SAS

AF:

0.00277

Gnomad FIN

AF:

0.000785

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00200

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.00178

AC:

AN:

26362

Hom.:

Cov.:

AF XY:

0.00178

AC XY:

AN XY:

26362

show subpopulations

African (AFR)

AF:

0.00210

AC:

AN:

6671

American (AMR)

AF:

0.00179

AC:

AN:

2798

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

640

East Asian (EAS)

AF:

0.000971

AC:

AN:

1030

South Asian (SAS)

AF:

0.00278

AC:

AN:

1078

European-Finnish (FIN)

AF:

0.000785

AC:

AN:

2549

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00200

AC:

AN:

11005

Other (OTH)

AF:

0.00

AC:

AN:

341

Age Distribution

Genome Hom

Variant carriers

<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

-0.94

CADD

Benign

3.2

(source)

DANN

Benign

0.34

PhyloP100

0.055

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