4-59201411-C-G

Variant names:

• chr4-59201411-C-G
• rs2009488

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 0.644 in 150,868 control chromosomes in the GnomAD database, including 31,378 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 0.64 (31378 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 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: 0.643 AC: 97010 AN: 150758 Hom.: 31331 Cov.: 30

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.644 AC: 97111 AN: 150868 Hom.: 31378 Cov.: 30 AF XY: 0.646 AC XY: 47468 AN XY: 73522

African (AFR) AF: 0.649 AC: 26702 AN: 41114

American (AMR) AF: 0.593 AC: 8994 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2264 AN: 3464

East Asian (EAS) AF: 0.609 AC: 3082 AN: 5060

South Asian (SAS) AF: 0.681 AC: 3267 AN: 4798

European-Finnish (FIN) AF: 0.681 AC: 6886 AN: 10116

Middle Eastern (MID) AF: 0.703 AC: 204 AN: 290

European-Non Finnish (NFE) AF: 0.645 AC: 43766 AN: 67864

Other (OTH) AF: 0.643 AC: 1350 AN: 2100

Alfa AF: 0.527 Hom.: 1431

Bravo AF: 0.633

Asia WGS AF: 0.699 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.32
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2009488; hg19: chr4-60067129;