rs10938397

Variant names:

• chr4-45180510-A-G
• rs10938397

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;