rs7938730

chr11-38423218-T-C

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 151,966 control chromosomes in the GnomAD database, including 12,100 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 (12100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56073 AN: 151848 Hom.: 12098 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.369 AC: 56084 AN: 151966 Hom.: 12100 Cov.: 32 AF XY: 0.362 AC XY: 26851 AN XY: 74264

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.0217

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.359

Alfa AF: 0.450 Hom.: 8490

Bravo AF: 0.347

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7938730; hg19: chr11-38444768;