5-14042267-A-C

Position:

• chr5-14042267-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.118 in 152,158 control chromosomes in the GnomAD database, including 1,130 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 0.12 (1130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17931 AN: 152040 Hom.: 1129 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.118 AC: 17929 AN: 152158 Hom.: 1130 Cov.: 32 AF XY: 0.115 AC XY: 8545 AN XY: 74400

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0810

Gnomad4 FIN AF: 0.0683

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.131

Alfa AF: 0.122 Hom.: 338

Bravo AF: 0.122

Asia WGS AF: 0.0990 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	9.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17228994; hg19: chr5-14042376;