chr2-41904383-G-A

Position:

• chr2-41904383-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 0.318 in 152,102 control chromosomes in the GnomAD database, including 8,445 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 0.32 (8445 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 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: 0.318 AC: 48270 AN: 151984 Hom.: 8445 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.318 AC: 48297 AN: 152102 Hom.: 8445 Cov.: 33 AF XY: 0.323 AC XY: 23997 AN XY: 74352

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.335

Alfa AF: 0.362 Hom.: 13483

Bravo AF: 0.301

Asia WGS AF: 0.460 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4952535; hg19: chr2-42131523;