rs2022767

Variant names:

• chr14-83001870-A-G
• rs2022767

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 0.0768 in 152,242 control chromosomes in the GnomAD database, including 548 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 0.077 (548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 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: 0.0769 AC: 11693 AN: 152124 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.0768 AC: 11686 AN: 152242 Hom.: 548 Cov.: 32 AF XY: 0.0777 AC XY: 5783 AN XY: 74438

African (AFR) AF: 0.0349 AC: 1451 AN: 41556

American (AMR) AF: 0.0698 AC: 1068 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3472

East Asian (EAS) AF: 0.0527 AC: 273 AN: 5184

South Asian (SAS) AF: 0.0590 AC: 285 AN: 4828

European-Finnish (FIN) AF: 0.146 AC: 1551 AN: 10594

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0944 AC: 6418 AN: 67994

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0905 Hom.: 455

Bravo AF: 0.0700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2022767; hg19: chr14-83468214;