rs6443523

Variant names:

• chr3-177987280-G-A
• rs6443523

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 0.362 in 151,796 control chromosomes in the GnomAD database, including 13,169 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 0.36 (13169 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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: 0.362 AC: 54877 AN: 151676 Hom.: 13115 Cov.: 30

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.362 AC: 55006 AN: 151796 Hom.: 13169 Cov.: 30 AF XY: 0.364 AC XY: 27027 AN XY: 74162

African (AFR) AF: 0.655 AC: 27096 AN: 41356

American (AMR) AF: 0.341 AC: 5206 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3001 AN: 5132

South Asian (SAS) AF: 0.475 AC: 2277 AN: 4792

European-Finnish (FIN) AF: 0.194 AC: 2050 AN: 10542

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13706 AN: 67920

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.251 Hom.: 9836

Bravo AF: 0.383

Asia WGS AF: 0.577 AC: 2005 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	0.36
DANN	Benign	0.42
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6443523; hg19: chr3-177705068;