rs1938670

Variant names:

• chr11-58360170-G-A
• rs1938670

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 0.313 in 151,804 control chromosomes in the GnomAD database, including 7,641 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 0.31 (7641 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

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 = 0.364 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: 0.314 AC: 47556 AN: 151686 Hom.: 7642 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.313 AC: 47567 AN: 151804 Hom.: 7641 Cov.: 30 AF XY: 0.309 AC XY: 22945 AN XY: 74170

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.293

Alfa AF: 0.357 Hom.: 9595

Bravo AF: 0.303

Asia WGS AF: 0.260 AC: 907 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	0.55
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938670; hg19: chr11-58127643;