rs9786140

Variant names:

• chrY-8634195-A-G
• rs9786140
• ENST00000650816.1:n.243-44162A>G

Your query was ambiguous. Multiple possible variants found:

• chrY-8634195-A-G
• chrY-8634195-A-T

Variant summary

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

The ENST00000650816.1(LINC00279):​n.243-44162A>G variant causes a intron change. 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 0.67 (0 hom., 21084 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: LINC00279 ENST00000650816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 8 publications found

Genes affected

LINC00279 (HGNC:38724): (long intergenic non-protein coding RNA 279)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00279	ENST00000650816.1		n.243-44162A>G		intron	N/A
	LINC00279	ENST00000651700.2		n.196-44162A>G		intron	N/A
	LINC00279	ENST00000651793.1		n.1448+968A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 21017 AN: 31579 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.986

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.637

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: 0.666 AC: 21084 AN: 31641 Hom.: 0 Cov.: 0 AF XY: 0.666 AC XY: 21084 AN XY: 31641

African (AFR) AF: 0.810 AC: 6463 AN: 7978

American (AMR) AF: 0.520 AC: 1785 AN: 3430

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 693 AN: 737

East Asian (EAS) AF: 1.00 AC: 1177 AN: 1177

South Asian (SAS) AF: 1.00 AC: 1268 AN: 1268

European-Finnish (FIN) AF: 0.976 AC: 3061 AN: 3135

Middle Eastern (MID) AF: 0.985 AC: 67 AN: 68

European-Non Finnish (NFE) AF: 0.472 AC: 6223 AN: 13183

Other (OTH) AF: 0.640 AC: 291 AN: 455

Alfa AF: 0.538 Hom.: 25137

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.28

Splicing

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

Other links and lift over

dbSNP: rs9786140; hg19: chrY-8502236;