11-98212912-G-C

Variant names:

• chr11-98212912-G-C
• rs2848488

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 0.77 in 151,912 control chromosomes in the GnomAD database, including 45,142 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 0.77 (45142 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.799 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: 0.770 AC: 116816 AN: 151794 Hom.: 45082 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.770 AC: 116941 AN: 151912 Hom.: 45142 Cov.: 31 AF XY: 0.769 AC XY: 57089 AN XY: 74260

African (AFR) AF: 0.795 AC: 32994 AN: 41476

American (AMR) AF: 0.669 AC: 10194 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3012 AN: 3468

East Asian (EAS) AF: 0.709 AC: 3669 AN: 5174

South Asian (SAS) AF: 0.820 AC: 3955 AN: 4822

European-Finnish (FIN) AF: 0.810 AC: 8542 AN: 10548

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.767 AC: 52083 AN: 67870

Other (OTH) AF: 0.754 AC: 1585 AN: 2102

Alfa AF: 0.690 Hom.: 2016

Bravo AF: 0.758

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.47
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2848488; hg19: chr11-98083640;