rs988131

Variant names:

• chr14-106776833-T-C
• rs988131

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 0.199 in 152,092 control chromosomes in the GnomAD database, including 3,489 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 0.20 (3489 hom., cov: 33)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

IGH (HGNC:5477):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30174 AN: 151974 Hom.: 3481 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.199 AC: 30211 AN: 152092 Hom.: 3489 Cov.: 33 AF XY: 0.198 AC XY: 14692 AN XY: 74354

African (AFR) AF: 0.324 AC: 13425 AN: 41438

American (AMR) AF: 0.186 AC: 2842 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3472

East Asian (EAS) AF: 0.186 AC: 964 AN: 5174

South Asian (SAS) AF: 0.160 AC: 772 AN: 4826

European-Finnish (FIN) AF: 0.128 AC: 1357 AN: 10592

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9569 AN: 67990

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.170 Hom.: 874

Bravo AF: 0.207

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.9
DANN	Benign	0.25
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs988131; hg19: chr14-107185072;