rs2949632

Variant names:

• chr4-106384408-G-A
• rs2949632

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 0.369 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.365

Alfa AF: 0.326 Hom.: 1500

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2949632; hg19: chr4-107305565;