chr14-106775945-T-A

Variant names:

• chr14-106775945-T-A
• rs10150241

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 152,144 control chromosomes in the GnomAD database, including 8,242 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 (8242 hom., cov: 33)
• Consequence: IGH intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGH		n.106775945T>A		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48312 AN: 152026 Hom.: 8217 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.318 AC: 48391 AN: 152144 Hom.: 8242 Cov.: 33 AF XY: 0.321 AC XY: 23864 AN XY: 74364

African (AFR) AF: 0.411 AC: 17035 AN: 41474

American (AMR) AF: 0.275 AC: 4210 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1279 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1799 AN: 5174

South Asian (SAS) AF: 0.495 AC: 2387 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2887 AN: 10580

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17828 AN: 68004

Other (OTH) AF: 0.307 AC: 649 AN: 2116

Alfa AF: 0.288 Hom.: 853

Bravo AF: 0.320

Asia WGS AF: 0.412 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10150241; hg19: chr14-107184184; COSMIC: COSV66753587;