9-102922983-A-G

Variant names:

• chr9-102922983-A-G
• rs10990381
• ENST00000430854.2:n.410A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430854.2(ENSG00000234269):​n.410A>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 0.258 in 151,882 control chromosomes in the GnomAD database, including 5,559 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 0.26 (5559 hom., cov: 31)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENSG00000234269 ENST00000430854.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 3 publications found

Genes affected

ENSG00000234269 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100421294		n.102922983A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234269	ENST00000430854.2	n.410A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39186 AN: 151756 Hom.: 5553 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.258 AC: 39227 AN: 151874 Hom.: 5559 Cov.: 31 AF XY: 0.261 AC XY: 19335 AN XY: 74222

African (AFR) AF: 0.184 AC: 7630 AN: 41478

American (AMR) AF: 0.370 AC: 5613 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1034 AN: 5146

South Asian (SAS) AF: 0.373 AC: 1799 AN: 4826

European-Finnish (FIN) AF: 0.214 AC: 2264 AN: 10576

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18743 AN: 67910

Other (OTH) AF: 0.302 AC: 637 AN: 2110

Alfa AF: 0.283 Hom.: 18005

Bravo AF: 0.268

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10990381; hg19: chr9-105685265;