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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGH		n.106776833T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;