chr14-55223031-G-A

Variant names:

• chr14-55223031-G-A
• rs10483640

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 0.0926 in 152,202 control chromosomes in the GnomAD database, including 1,780 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 0.093 (1780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 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: 0.0924 AC: 14053 AN: 152084 Hom.: 1769 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0698

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.00509

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.00803

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0926 AC: 14101 AN: 152202 Hom.: 1780 Cov.: 32 AF XY: 0.0899 AC XY: 6692 AN XY: 74418

African (AFR) AF: 0.282 AC: 11707 AN: 41496

American (AMR) AF: 0.0475 AC: 726 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3470

East Asian (EAS) AF: 0.0694 AC: 359 AN: 5174

South Asian (SAS) AF: 0.0636 AC: 307 AN: 4824

European-Finnish (FIN) AF: 0.00509 AC: 54 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.00803 AC: 546 AN: 68016

Other (OTH) AF: 0.0775 AC: 164 AN: 2116

Alfa AF: 0.0169 Hom.: 38

Bravo AF: 0.103

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.62
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs10483640; hg19: chr14-55689749;