rs7140253

Variant names:

• chr14-106825769-A-G
• rs7140253

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 0.279 in 152,024 control chromosomes in the GnomAD database, including 9,758 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 0.28 (9758 hom., cov: 32)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 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: 0.278 AC: 42286 AN: 151906 Hom.: 9719 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.279 AC: 42374 AN: 152024 Hom.: 9758 Cov.: 32 AF XY: 0.275 AC XY: 20444 AN XY: 74310

African (AFR) AF: 0.639 AC: 26474 AN: 41418

American (AMR) AF: 0.179 AC: 2742 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3466

East Asian (EAS) AF: 0.246 AC: 1276 AN: 5178

South Asian (SAS) AF: 0.202 AC: 973 AN: 4816

European-Finnish (FIN) AF: 0.120 AC: 1264 AN: 10570

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8575 AN: 67974

Other (OTH) AF: 0.262 AC: 555 AN: 2116

Alfa AF: 0.161 Hom.: 1827

Bravo AF: 0.297

Asia WGS AF: 0.232 AC: 810 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	5.4
DANN	Benign	0.31
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7140253; hg19: chr14-107233999;