2-41904383-G-A

Variant names:

• chr2-41904383-G-A
• rs4952535

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 0.318 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.172 AC: 7153 AN: 41514

American (AMR) AF: 0.335 AC: 5117 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3466

East Asian (EAS) AF: 0.362 AC: 1875 AN: 5180

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4816

European-Finnish (FIN) AF: 0.405 AC: 4273 AN: 10548

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25346 AN: 67968

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.350 Hom.: 19308

Bravo AF: 0.301

Asia WGS AF: 0.460 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs4952535; hg19: chr2-42131523;