14-105745936-C-T

Variant names:

• chr14-105745936-C-T
• rs11160868

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 0.318 in 144,126 control chromosomes in the GnomAD database, including 7,766 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 0.32 (7766 hom., cov: 28)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.493 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: 0.318 AC: 45778 AN: 144024 Hom.: 7749 Cov.: 28

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.233

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.318 AC: 45818 AN: 144126 Hom.: 7766 Cov.: 28 AF XY: 0.330 AC XY: 23151 AN XY: 70120

African (AFR) AF: 0.251 AC: 9707 AN: 38618

American (AMR) AF: 0.503 AC: 7194 AN: 14304

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 710 AN: 3410

East Asian (EAS) AF: 0.371 AC: 1621 AN: 4374

South Asian (SAS) AF: 0.388 AC: 1649 AN: 4254

European-Finnish (FIN) AF: 0.420 AC: 4214 AN: 10034

Middle Eastern (MID) AF: 0.238 AC: 48 AN: 202

European-Non Finnish (NFE) AF: 0.300 AC: 19828 AN: 66072

Other (OTH) AF: 0.317 AC: 630 AN: 1988

Alfa AF: 0.145 Hom.: 247

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs11160868; hg19: chr14-106212273;