chr9-126520078-G-A

Position:

• chr9-126520078-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000624132.1(ENSG00000279137):​n.1239G>A 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 0.225 in 152,188 control chromosomes in the GnomAD database, including 5,010 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 0.23 (5010 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: ENST00000624132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376276	XR_930358.4	n.1945G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000624132.1	n.1239G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34213 AN: 152054 Hom.: 4992 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.225 AC: 34275 AN: 152172 Hom.: 5010 Cov.: 32 AF XY: 0.228 AC XY: 16967 AN XY: 74396

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.235

Alfa AF: 0.158 Hom.: 1307

Bravo AF: 0.250

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs885618; hg19: chr9-129282357;