rs2753571

Variant names:

• chr14-105786362-C-A
• rs2753571

Your query was ambiguous. Multiple possible variants found:

• chr14-105786362-C-A
• chr14-105786362-C-G
• chr14-105786362-C-T

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 0.41 in 149,292 control chromosomes in the GnomAD database, including 13,982 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 0.41 (13982 hom., cov: 32)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.410 AC: 61109 AN: 149188 Hom.: 13947 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.410 AC: 61190 AN: 149292 Hom.: 13982 Cov.: 32 AF XY: 0.425 AC XY: 30905 AN XY: 72770

African (AFR) AF: 0.403 AC: 16351 AN: 40558

American (AMR) AF: 0.551 AC: 8052 AN: 14622

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 837 AN: 3464

East Asian (EAS) AF: 0.984 AC: 4631 AN: 4704

South Asian (SAS) AF: 0.558 AC: 2512 AN: 4500

European-Finnish (FIN) AF: 0.444 AC: 4681 AN: 10546

Middle Eastern (MID) AF: 0.301 AC: 71 AN: 236

European-Non Finnish (NFE) AF: 0.339 AC: 22932 AN: 67696

Other (OTH) AF: 0.410 AC: 843 AN: 2054

Alfa AF: 0.201 Hom.: 374

Bravo AF: 0.422

Asia WGS AF: 0.744 AC: 2549 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.44
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2753571; hg19: chr14-106252699;