chr5-14042267-A-C

Variant names:

• chr5-14042267-A-C
• rs17228994

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.111 AC: 4621 AN: 41494

American (AMR) AF: 0.109 AC: 1660 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3472

East Asian (EAS) AF: 0.121 AC: 626 AN: 5186

South Asian (SAS) AF: 0.0810 AC: 390 AN: 4812

European-Finnish (FIN) AF: 0.0683 AC: 725 AN: 10612

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8898 AN: 67976

Other (OTH) AF: 0.131 AC: 276 AN: 2102

Alfa AF: 0.124 Hom.: 2088

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs17228994; hg19: chr5-14042376;