chr14-38214056-C-T

Variant names:

• chr14-38214056-C-T
• rs11622412

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 0.0919 in 152,186 control chromosomes in the GnomAD database, including 985 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 0.092 (985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.0918 AC: 13957 AN: 152068 Hom.: 982 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.0660

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0919 AC: 13987 AN: 152186 Hom.: 985 Cov.: 32 AF XY: 0.0943 AC XY: 7016 AN XY: 74404

African (AFR) AF: 0.140 AC: 5791 AN: 41512

American (AMR) AF: 0.101 AC: 1546 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3468

East Asian (EAS) AF: 0.356 AC: 1835 AN: 5158

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4828

European-Finnish (FIN) AF: 0.0721 AC: 764 AN: 10590

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3253 AN: 68014

Other (OTH) AF: 0.0819 AC: 173 AN: 2112

Alfa AF: 0.0759 Hom.: 1212

Bravo AF: 0.0991

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.51
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs11622412; hg19: chr14-38683261;