5-4267013-G-C

Variant names:

• chr5-4267013-G-C
• rs463803

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 0.804 in 152,144 control chromosomes in the GnomAD database, including 49,351 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 0.80 (49351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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: 0.804 AC: 122275 AN: 152024 Hom.: 49310 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.804 AC: 122376 AN: 152144 Hom.: 49351 Cov.: 32 AF XY: 0.805 AC XY: 59862 AN XY: 74366

African (AFR) AF: 0.771 AC: 32010 AN: 41518

American (AMR) AF: 0.796 AC: 12156 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2729 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4049 AN: 5148

South Asian (SAS) AF: 0.828 AC: 3995 AN: 4822

European-Finnish (FIN) AF: 0.857 AC: 9081 AN: 10602

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.820 AC: 55744 AN: 67990

Other (OTH) AF: 0.787 AC: 1660 AN: 2108

Alfa AF: 0.810 Hom.: 5857

Bravo AF: 0.794

Asia WGS AF: 0.794 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.33
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs463803; hg19: chr5-4267126;