rs943423

Variant names:

• chr9-134545337-G-A
• rs943423
• ENST00000435284.3:n.1407G>A

Variant summary

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

The ENST00000435284.3(ENSG00000228877):​n.1407G>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 0.698 in 152,032 control chromosomes in the GnomAD database, including 37,066 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 0.70 (37063 hom., cov: 32)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: ENSG00000228877 ENST00000435284.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 9 publications found

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.*74G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.3	n.1407G>A		non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000228877	ENST00000745249.1	n.*74G>A		downstream_gene_variant
ENSG00000228877	ENST00000745250.1	n.*74G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106001 AN: 151908 Hom.: 37016 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.679

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 AF XY: 1.00 AC XY: 6 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) AC: 0 AN: 0

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: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.698 AC: 106107 AN: 152026 Hom.: 37063 Cov.: 32 AF XY: 0.699 AC XY: 51958 AN XY: 74318

African (AFR) AF: 0.704 AC: 29192 AN: 41448

American (AMR) AF: 0.719 AC: 10990 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2326 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3884 AN: 5170

South Asian (SAS) AF: 0.495 AC: 2379 AN: 4810

European-Finnish (FIN) AF: 0.777 AC: 8214 AN: 10578

Middle Eastern (MID) AF: 0.659 AC: 191 AN: 290

European-Non Finnish (NFE) AF: 0.689 AC: 46854 AN: 67958

Other (OTH) AF: 0.676 AC: 1423 AN: 2104

Alfa AF: 0.690 Hom.: 62328

Bravo AF: 0.701

Asia WGS AF: 0.638 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.82
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs943423; hg19: chr9-137437183;