4-106384408-G-A

Variant names:

• chr4-106384408-G-A
• rs2949632

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 0.369 in 150,884 control chromosomes in the GnomAD database, including 11,271 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 0.37 (11271 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 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: 0.369 AC: 55574 AN: 150772 Hom.: 11256 Cov.: 30

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.369 AC: 55632 AN: 150884 Hom.: 11271 Cov.: 30 AF XY: 0.365 AC XY: 26904 AN XY: 73626

African (AFR) AF: 0.555 AC: 22770 AN: 41004

American (AMR) AF: 0.302 AC: 4578 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1118 AN: 3456

East Asian (EAS) AF: 0.277 AC: 1419 AN: 5120

South Asian (SAS) AF: 0.284 AC: 1356 AN: 4780

European-Finnish (FIN) AF: 0.271 AC: 2784 AN: 10256

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20441 AN: 67794

Other (OTH) AF: 0.365 AC: 764 AN: 2094

Alfa AF: 0.332 Hom.: 1614

Bravo AF: 0.378

Asia WGS AF: 0.291 AC: 1000 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.63
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2949632; hg19: chr4-107305565;