chrY-9903745-T-C

Variant names:

• chrY-9903745-T-C
• rs2337080
• ENST00000841136.1:n.1037A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

Genes affected

ENSG00000309435 (HGNC:):

ACMG classification

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	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: 46 AN: 26337 Hom.: 0 Cov.: 0

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: 47 AN: 26362 Hom.: 0 Cov.: 0 AF XY: 0.00178 AC XY: 47 AN XY: 26362

African (AFR) AF: 0.00210 AC: 14 AN: 6671

American (AMR) AF: 0.00179 AC: 5 AN: 2798

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 640

East Asian (EAS) AF: 0.000971 AC: 1 AN: 1030

South Asian (SAS) AF: 0.00278 AC: 3 AN: 1078

European-Finnish (FIN) AF: 0.000785 AC: 2 AN: 2549

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 60

European-Non Finnish (NFE) AF: 0.00200 AC: 22 AN: 11005

Other (OTH) AF: 0.00 AC: 0 AN: 341

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
DANN	Benign	0.34
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs2337080; hg19: chrY-9741354; COSMIC: COSV100164344;