chr5-6521724-A-C

Variant names:

• chr5-6521724-A-C
• rs563624

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 0.442 in 152,148 control chromosomes in the GnomAD database, including 15,347 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 (15347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.442 AC: 67211 AN: 152030 Hom.: 15324 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.442 AC: 67288 AN: 152148 Hom.: 15347 Cov.: 32 AF XY: 0.439 AC XY: 32656 AN XY: 74370

African (AFR) AF: 0.573 AC: 23775 AN: 41508

American (AMR) AF: 0.368 AC: 5615 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1608 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5178

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4818

European-Finnish (FIN) AF: 0.418 AC: 4426 AN: 10588

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27549 AN: 67990

Other (OTH) AF: 0.428 AC: 904 AN: 2112

Alfa AF: 0.416 Hom.: 57107

Bravo AF: 0.447

Asia WGS AF: 0.326 AC: 1138 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	4.7
DANN	Benign	0.61
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs563624; hg19: chr5-6521837;