rs9656709

Variant names:

• chr7-55656752-A-C
• rs9656709
• ENST00000432235.1:n.*16T>G

Variant summary

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

The ENST00000432235.1(ENSG00000231317):​n.*16T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,128 control chromosomes in the GnomAD database, including 16,591 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 0.46 (16548 hom., cov: 31)
  • Exomes 𝑓: 0.59 (43 hom.)
• Consequence: ENSG00000231317 ENST00000432235.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

ENSG00000231317 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

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
ENSG00000231317	ENST00000432235.1	n.*16T>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70277 AN: 151780 Hom.: 16549 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.512

GnomAD4 exome AF: 0.591 AC: 136 AN: 230 Hom.: 43 Cov.: 0 AF XY: 0.537 AC XY: 72 AN XY: 134

Gnomad4 AFR exome AF: 0.571

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.463 AC: 70305 AN: 151898 Hom.: 16548 Cov.: 31 AF XY: 0.456 AC XY: 33839 AN XY: 74250

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.510

Alfa AF: 0.490 Hom.: 10389

Bravo AF: 0.466

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9656709; hg19: chr7-55724445;