chr8-53584302-G-A

Variant names:

• chr8-53584302-G-A
• rs11778957

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 0.435 in 152,020 control chromosomes in the GnomAD database, including 17,662 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 0.44 (17662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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: 0.436 AC: 66224 AN: 151902 Hom.: 17671 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.435 AC: 66201 AN: 152020 Hom.: 17662 Cov.: 32 AF XY: 0.429 AC XY: 31846 AN XY: 74282

African (AFR) AF: 0.125 AC: 5174 AN: 41470

American (AMR) AF: 0.441 AC: 6734 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2067 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1443 AN: 4810

European-Finnish (FIN) AF: 0.529 AC: 5571 AN: 10540

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41668 AN: 67972

Other (OTH) AF: 0.480 AC: 1013 AN: 2110

Alfa AF: 0.511 Hom.: 3136

Bravo AF: 0.420

Asia WGS AF: 0.329 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs11778957; hg19: chr8-54496862;