rs7067387

Variant names:

• chrY-9973185-C-T
• rs7067387
• ENST00000651645.1:n.1003+16005G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000651645.1(ENSG00000290344):​n.1003+16005G>A 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 0.99 (0 hom., 32502 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290344 ENST00000651645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 1 publications found

Genes affected

ENSG00000290344 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651645.1. 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
	ENSG00000290344	ENST00000651645.1		n.1003+16005G>A		intron	N/A
	ENSG00000290344	ENST00000787703.1		n.422-18493G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.994 AC: 32435 AN: 32644 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.993

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.994 AC: 32502 AN: 32711 Hom.: 0 Cov.: 0 AF XY: 0.994 AC XY: 32502 AN XY: 32711

African (AFR) AF: 0.996 AC: 8354 AN: 8388

American (AMR) AF: 0.995 AC: 3508 AN: 3524

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 762 AN: 762

East Asian (EAS) AF: 1.00 AC: 1206 AN: 1206

South Asian (SAS) AF: 1.00 AC: 1398 AN: 1398

European-Finnish (FIN) AF: 1.00 AC: 3270 AN: 3270

Middle Eastern (MID) AF: 1.00 AC: 73 AN: 73

European-Non Finnish (NFE) AF: 0.990 AC: 13294 AN: 13435

Other (OTH) AF: 0.993 AC: 438 AN: 441

Alfa AF: 0.911 Hom.: 12702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7067387; hg19: chrY-9810794;