rs4607576

Variant names:

• chr8-109153807-G-A
• rs4607576

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 0.327 in 152,060 control chromosomes in the GnomAD database, including 8,667 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 0.33 (8667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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: 0.327 AC: 49653 AN: 151940 Hom.: 8661 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.327 AC: 49680 AN: 152060 Hom.: 8667 Cov.: 32 AF XY: 0.332 AC XY: 24707 AN XY: 74334

African (AFR) AF: 0.222 AC: 9206 AN: 41486

American (AMR) AF: 0.432 AC: 6602 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2438 AN: 5162

South Asian (SAS) AF: 0.429 AC: 2067 AN: 4818

European-Finnish (FIN) AF: 0.393 AC: 4149 AN: 10564

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23305 AN: 67962

Other (OTH) AF: 0.313 AC: 661 AN: 2110

Alfa AF: 0.328 Hom.: 1215

Bravo AF: 0.325

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.014
DANN	Benign	0.54
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4607576; hg19: chr8-110166036;