chr14-78156180-A-G

Variant names:

• chr14-78156180-A-G
• rs17754467

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 0.18 in 152,036 control chromosomes in the GnomAD database, including 2,797 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 0.18 (2797 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 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: 0.180 AC: 27291 AN: 151918 Hom.: 2796 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.180 AC: 27307 AN: 152036 Hom.: 2797 Cov.: 32 AF XY: 0.178 AC XY: 13245 AN XY: 74304

African (AFR) AF: 0.104 AC: 4310 AN: 41472

American (AMR) AF: 0.173 AC: 2642 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.00541 AC: 28 AN: 5178

South Asian (SAS) AF: 0.200 AC: 960 AN: 4808

European-Finnish (FIN) AF: 0.208 AC: 2196 AN: 10558

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15603 AN: 67958

Other (OTH) AF: 0.202 AC: 427 AN: 2114

Alfa AF: 0.203 Hom.: 919

Bravo AF: 0.172

Asia WGS AF: 0.103 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.44
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs17754467; hg19: chr14-78622523;