chr2-38552247-G-A

Position:

• chr2-38552247-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 0.278 in 152,080 control chromosomes in the GnomAD database, including 7,312 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 0.28 (7312 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42269 AN: 151962 Hom.: 7281 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.278 AC: 42333 AN: 152080 Hom.: 7312 Cov.: 32 AF XY: 0.272 AC XY: 20249 AN XY: 74356

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.236

Alfa AF: 0.240 Hom.: 1420

Bravo AF: 0.295

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6727476; hg19: chr2-38779389;