rs10938397

Positions:

• chr4-45180510-A-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 0.374 in 151,772 control chromosomes in the GnomAD database, including 11,281 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 (11281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 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: 0.374 AC: 56777 AN: 151654 Hom.: 11280 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.374 AC: 56787 AN: 151772 Hom.: 11281 Cov.: 32 AF XY: 0.376 AC XY: 27916 AN XY: 74186

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.377

Alfa AF: 0.415 Hom.: 14122

Bravo AF: 0.361

Asia WGS AF: 0.302 AC: 1049 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10938397; hg19: chr4-45182527;