rs3932338

Positions:

• chr5-23742867-G-A
• chr5-23742867-G-T

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 0.487 in 151,970 control chromosomes in the GnomAD database, including 19,729 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 0.49 (19729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 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: 0.487 AC: 73927 AN: 151852 Hom.: 19732 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.487 AC: 73944 AN: 151970 Hom.: 19729 Cov.: 32 AF XY: 0.488 AC XY: 36231 AN XY: 74238

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.523

Alfa AF: 0.578 Hom.: 42467

Bravo AF: 0.478

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3932338; hg19: chr5-23742976;