rs1938670

Positions:

• chr11-58360170-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;