14-106189185-A-T

Variant names:

• chr14-106189185-A-T
• rs1981496

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 0.0856 in 150,552 control chromosomes in the GnomAD database, including 807 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 0.086 (807 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 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: 0.0855 AC: 12859 AN: 150446 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0308

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0761

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0856 AC: 12894 AN: 150552 Hom.: 807 Cov.: 32 AF XY: 0.0886 AC XY: 6511 AN XY: 73486

African (AFR) AF: 0.0520 AC: 2132 AN: 41026

American (AMR) AF: 0.104 AC: 1550 AN: 14934

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3462

East Asian (EAS) AF: 0.127 AC: 617 AN: 4846

South Asian (SAS) AF: 0.0881 AC: 413 AN: 4686

European-Finnish (FIN) AF: 0.148 AC: 1571 AN: 10588

Middle Eastern (MID) AF: 0.0328 AC: 8 AN: 244

European-Non Finnish (NFE) AF: 0.0929 AC: 6299 AN: 67770

Other (OTH) AF: 0.0792 AC: 165 AN: 2084

Alfa AF: 0.0347 Hom.: 37

Bravo AF: 0.0828

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.37
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1981496; hg19: chr14-106645846;