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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290344	ENST00000651645.1	n.1003+16005G>A		intron_variant	Intron 9 of 9
ENSG00000290344	ENST00000787703.1	n.422-18493G>A		intron_variant	Intron 4 of 4

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 v4.3

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;