chr14-41233395-G-A

Variant names:

• chr14-41233395-G-A
• rs1612141

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 0.245 in 152,000 control chromosomes in the GnomAD database, including 4,845 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 0.24 (4845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 13 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37155 AN: 151882 Hom.: 4827 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.245 AC: 37213 AN: 152000 Hom.: 4845 Cov.: 32 AF XY: 0.250 AC XY: 18549 AN XY: 74276

African (AFR) AF: 0.288 AC: 11923 AN: 41460

American (AMR) AF: 0.324 AC: 4940 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.173 AC: 895 AN: 5164

South Asian (SAS) AF: 0.144 AC: 692 AN: 4808

European-Finnish (FIN) AF: 0.316 AC: 3338 AN: 10552

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14327 AN: 67976

Other (OTH) AF: 0.241 AC: 508 AN: 2108

Alfa AF: 0.222 Hom.: 12408

Bravo AF: 0.249

Asia WGS AF: 0.184 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.48
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1612141; hg19: chr14-41702598;