rs663924

Variant names:

• chr2-234025542-A-G
• rs663924

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 0.303 in 151,748 control chromosomes in the GnomAD database, including 7,675 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 0.30 (7675 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 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: 0.303 AC: 45989 AN: 151632 Hom.: 7677 Cov.: 29

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.303 AC: 45991 AN: 151748 Hom.: 7675 Cov.: 29 AF XY: 0.308 AC XY: 22827 AN XY: 74120

African (AFR) AF: 0.169 AC: 7005 AN: 41358

American (AMR) AF: 0.270 AC: 4121 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1084 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2752 AN: 5142

South Asian (SAS) AF: 0.397 AC: 1897 AN: 4780

European-Finnish (FIN) AF: 0.393 AC: 4138 AN: 10516

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23971 AN: 67908

Other (OTH) AF: 0.320 AC: 673 AN: 2100

Alfa AF: 0.338 Hom.: 17126

Bravo AF: 0.287

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.26
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs663924; hg19: chr2-234934186;