4-8641359-C-A

Variant names:

• chr4-8641359-C-A
• rs12510524

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 0.0354 in 152,370 control chromosomes in the GnomAD database, including 201 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 0.035 (201 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0893 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: 0.0354 AC: 5388 AN: 152252 Hom.: 201 Cov.: 34

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00883

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0354 AC: 5392 AN: 152370 Hom.: 201 Cov.: 34 AF XY: 0.0353 AC XY: 2633 AN XY: 74508

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0316

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00883

Gnomad4 OTH AF: 0.0269

Alfa AF: 0.00614 Hom.: 3

Bravo AF: 0.0401

Asia WGS AF: 0.0590 AC: 205 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	0.034
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12510524; hg19: chr4-8643085;