rs1938672

chr11-58361580-C-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 0.285 in 151,710 control chromosomes in the GnomAD database, including 6,780 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 0.28 (6780 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

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 = 0.365 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: 0.285 AC: 43195 AN: 151590 Hom.: 6781 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.285 AC: 43201 AN: 151710 Hom.: 6780 Cov.: 31 AF XY: 0.282 AC XY: 20896 AN XY: 74100

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.275

Alfa AF: 0.351 Hom.: 12707

Bravo AF: 0.270

Asia WGS AF: 0.255 AC: 890 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	0.98
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938672; hg19: chr11-58129053;