chr2-204263298-G-A

Variant names:

• chr2-204263298-G-A
• rs6738181

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 0.3 in 151,966 control chromosomes in the GnomAD database, including 7,590 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 (7590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 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: 0.299 AC: 45476 AN: 151848 Hom.: 7579 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.300 AC: 45518 AN: 151966 Hom.: 7590 Cov.: 32 AF XY: 0.300 AC XY: 22269 AN XY: 74282

African (AFR) AF: 0.451 AC: 18698 AN: 41424

American (AMR) AF: 0.218 AC: 3333 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3466

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5168

South Asian (SAS) AF: 0.269 AC: 1292 AN: 4810

European-Finnish (FIN) AF: 0.296 AC: 3123 AN: 10556

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16192 AN: 67962

Other (OTH) AF: 0.304 AC: 638 AN: 2100

Alfa AF: 0.290 Hom.: 5264

Bravo AF: 0.299

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs6738181; hg19: chr2-205128021;