rs6432018

Variant names:

• chr2-9581767-C-A
• rs6432018

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 0.591 in 152,050 control chromosomes in the GnomAD database, including 28,884 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 0.59 (28884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 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: 0.591 AC: 89802 AN: 151930 Hom.: 28844 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.591 AC: 89897 AN: 152050 Hom.: 28884 Cov.: 32 AF XY: 0.579 AC XY: 43033 AN XY: 74314

African (AFR) AF: 0.815 AC: 33834 AN: 41490

American (AMR) AF: 0.438 AC: 6687 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2234 AN: 3468

East Asian (EAS) AF: 0.0605 AC: 313 AN: 5174

South Asian (SAS) AF: 0.383 AC: 1850 AN: 4824

European-Finnish (FIN) AF: 0.519 AC: 5468 AN: 10544

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37587 AN: 67970

Other (OTH) AF: 0.597 AC: 1260 AN: 2112

Alfa AF: 0.560 Hom.: 109674

Bravo AF: 0.594

Asia WGS AF: 0.297 AC: 1034 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.68
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs6432018; hg19: chr2-9721896;