rs9656709

Positions:

• chr7-55656752-A-C

Variant summary

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

The 7-55656752-A-C 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: ENST00000432235.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000432235.1			downstream_gene_variant

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;