rs1928007

Variant names:

• chr13-70236091-G-A
• rs1928007

Your query was ambiguous. Multiple possible variants found:

• chr13-70236091-G-A
• chr13-70236091-G-C
• chr13-70236091-G-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 0.839 in 151,922 control chromosomes in the GnomAD database, including 54,250 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 0.84 (54250 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.839 AC: 127323 AN: 151806 Hom.: 54203 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.839 AC: 127424 AN: 151922 Hom.: 54250 Cov.: 33 AF XY: 0.841 AC XY: 62440 AN XY: 74240

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.839

Alfa AF: 0.869 Hom.: 7970

Bravo AF: 0.827

Asia WGS AF: 0.910 AC: 3122 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
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: rs1928007; hg19: chr13-70810223;