rs1022772

Positions:

• chr9-38435828-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635962.1(ENSG00000291061):​n.289T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0332 in 152,314 control chromosomes in the GnomAD database, including 181 homozygotes. 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 0.033 (181 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000635962.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376041	XR_007061486.1	n.489T>G		non_coding_transcript_exon_variant	3/9
LOC105376041	XR_007061484.1	n.850T>G		non_coding_transcript_exon_variant	2/6
LOC105376041	XR_007061485.1	n.489T>G		non_coding_transcript_exon_variant	3/7
LOC105376041	XR_007061487.1	n.489T>G		non_coding_transcript_exon_variant	3/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000635962.1	n.289T>G		non_coding_transcript_exon_variant	2/10	5
	ENST00000637760.3	n.291T>G		non_coding_transcript_exon_variant	2/6	5
	ENST00000685989.1	n.289T>G		non_coding_transcript_exon_variant	2/11

Frequencies

GnomAD3 genomes AF: 0.0330 AC: 5017 AN: 152198 Hom.: 177 Cov.: 33

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00886

Gnomad OTH AF: 0.0368

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0332 AC: 5052 AN: 152314 Hom.: 181 Cov.: 33 AF XY: 0.0357 AC XY: 2657 AN XY: 74472

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.0937

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0182

Gnomad4 NFE AF: 0.00886

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0188 Hom.: 91

Bravo AF: 0.0405

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1022772; hg19: chr9-38435825;