22-16871334-A-G

Variant names:

• chr22-16871334-A-G
• rs4006314
• ENST00000442403.1:n.*208A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000821830.1(ENSG00000237689):​n.*53A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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 0.49 (0 hom., cov: 50)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000237689 ENST00000821830.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 2 publications found

Genes affected

ENSG00000237689 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821830.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237689	ENST00000442403.1	TSL:5	n.*208A>G		downstream_gene	N/A
	ENSG00000237689	ENST00000821830.1		n.*53A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.488 AC: 68527 AN: 140390 Hom.: 0 Cov.: 50

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.486

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.488 AC: 68559 AN: 140458 Hom.: 0 Cov.: 50 AF XY: 0.487 AC XY: 33406 AN XY: 68626

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.479 AC: 17773 AN: 37122

American (AMR) AF: 0.492 AC: 7050 AN: 14318

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1579 AN: 3210

East Asian (EAS) AF: 0.487 AC: 2298 AN: 4720

South Asian (SAS) AF: 0.493 AC: 2242 AN: 4546

European-Finnish (FIN) AF: 0.495 AC: 4991 AN: 10078

Middle Eastern (MID) AF: 0.485 AC: 133 AN: 274

European-Non Finnish (NFE) AF: 0.491 AC: 31156 AN: 63436

Other (OTH) AF: 0.486 AC: 931 AN: 1914

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.480 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.65
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4006314;

hg19: chr22-17352224;

COSMIC: COSV71365362;