rs4077632

Positions:

• chr9-78548557-G-A

Variant summary

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

The variant allele was found at a frequency of 0.515 in 151,942 control chromosomes in the GnomAD database, including 22,948 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 0.52 (22948 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78296 AN: 151824 Hom.: 22941 Cov.: 31

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.523

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.515 AC: 78317 AN: 151942 Hom.: 22948 Cov.: 31 AF XY: 0.514 AC XY: 38140 AN XY: 74250

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.522

Alfa AF: 0.608 Hom.: 19398

Bravo AF: 0.490

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077632; hg19: chr9-81163473;