rs638893

Positions:

• chr11-118827828-G-A
• chr11-118827828-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;