rs638893

Variant names:

• chr11-118827828-G-A
• rs638893

Your query was ambiguous. Multiple possible variants found:

• chr11-118827828-G-A
• chr11-118827828-G-C
• chr11-118827828-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 0.789 in 152,146 control chromosomes in the GnomAD database, including 47,921 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 0.79 (47921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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: 0.789 AC: 119972 AN: 152028 Hom.: 47881 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.789 AC: 120065 AN: 152146 Hom.: 47921 Cov.: 32 AF XY: 0.791 AC XY: 58833 AN XY: 74368

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.820

Alfa AF: 0.816 Hom.: 23171

Bravo AF: 0.784

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs638893; hg19: chr11-118698537;