rs3923518

Positions:

• chr3-38844922-C-A
• chr3-38844922-C-G

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 0.231 in 152,004 control chromosomes in the GnomAD database, including 4,166 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 0.23 (4166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 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: 0.231 AC: 35059 AN: 151886 Hom.: 4169 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.231 AC: 35069 AN: 152004 Hom.: 4166 Cov.: 32 AF XY: 0.230 AC XY: 17079 AN XY: 74326

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.220

Alfa AF: 0.244 Hom.: 7746

Bravo AF: 0.234

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3923518; hg19: chr3-38886413;