rs4077632

Variant names:

• chr9-78548557-G-A
• rs4077632

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.251 AC: 10387 AN: 41412

American (AMR) AF: 0.513 AC: 7839 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1089 AN: 5146

South Asian (SAS) AF: 0.478 AC: 2300 AN: 4814

European-Finnish (FIN) AF: 0.695 AC: 7340 AN: 10558

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

European-Non Finnish (NFE) AF: 0.671 AC: 45594 AN: 67956

Other (OTH) AF: 0.522 AC: 1102 AN: 2112

Alfa AF: 0.605 Hom.: 27165

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
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4077632; hg19: chr9-81163473;