rs1938670

Variant names:

• chr11-58360170-G-A
• rs1938670

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.257 AC: 10649 AN: 41414

American (AMR) AF: 0.259 AC: 3941 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3464

East Asian (EAS) AF: 0.147 AC: 753 AN: 5136

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4816

European-Finnish (FIN) AF: 0.339 AC: 3574 AN: 10550

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24971 AN: 67878

Other (OTH) AF: 0.293 AC: 617 AN: 2106

Alfa AF: 0.352 Hom.: 12128

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1938670; hg19: chr11-58127643;