chr11-98252776-T-C

Variant names:

• chr11-98252776-T-C
• rs2848547

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 0.382 in 151,886 control chromosomes in the GnomAD database, including 11,269 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 0.38 (11269 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.452 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: 0.382 AC: 57946 AN: 151768 Hom.: 11258 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.382 AC: 57996 AN: 151886 Hom.: 11269 Cov.: 31 AF XY: 0.389 AC XY: 28843 AN XY: 74242

African (AFR) AF: 0.348 AC: 14436 AN: 41430

American (AMR) AF: 0.337 AC: 5145 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2164 AN: 5156

South Asian (SAS) AF: 0.468 AC: 2252 AN: 4810

European-Finnish (FIN) AF: 0.527 AC: 5554 AN: 10530

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26007 AN: 67904

Other (OTH) AF: 0.383 AC: 808 AN: 2112

Alfa AF: 0.362 Hom.: 1696

Bravo AF: 0.363

Asia WGS AF: 0.442 AC: 1533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2848547; hg19: chr11-98123504;