rs6738181

chr2-204263298-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.304

Alfa AF: 0.262 Hom.: 1758

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6738181; hg19: chr2-205128021;