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).

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
LINC00279	ENST00000650816.1	n.243-44162A>G		intron_variant	Intron 1 of 11
LINC00279	ENST00000651700.2	n.196-44162A>G		intron_variant	Intron 1 of 7
LINC00279	ENST00000651793.1	n.1448+968A>G		intron_variant	Intron 5 of 6

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 v4.3

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;