chr2-218838575-A-C

Variant names:

• chr2-218838575-A-C
• rs730947

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 0.102 in 151,720 control chromosomes in the GnomAD database, including 1,038 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 0.10 (1038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 13 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 (EAS) allele frequency at 95% confidence interval = 0.219 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: 0.102 AC: 15535 AN: 151604 Hom.: 1036 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.102 AC: 15542 AN: 151720 Hom.: 1038 Cov.: 32 AF XY: 0.100 AC XY: 7439 AN XY: 74180

African (AFR) AF: 0.0255 AC: 1050 AN: 41124

American (AMR) AF: 0.138 AC: 2110 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1191 AN: 5184

South Asian (SAS) AF: 0.103 AC: 499 AN: 4824

European-Finnish (FIN) AF: 0.0698 AC: 735 AN: 10536

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8993 AN: 67994

Other (OTH) AF: 0.106 AC: 224 AN: 2110

Alfa AF: 0.129 Hom.: 2451

Bravo AF: 0.106

Asia WGS AF: 0.139 AC: 481 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.83
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs730947; hg19: chr2-219703298;