rs3885584

Variant names:

• chr22-46146500-G-A
• rs3885584
• ENST00000846710.1:n.328+4567C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-46146500-G-A
• chr22-46146500-G-C
• chr22-46146500-G-T

Variant summary

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

The ENST00000846710.1(ENSG00000310037):​n.328+4567C>T variant causes a intron 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 0.0017 (0 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000310037 ENST00000846710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 2 publications found

Genes affected

ENSG00000310037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846710.1. 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
	ENSG00000310037	ENST00000846710.1		n.328+4567C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00168 AC: 166 AN: 99068 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.000599

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000650

Gnomad ASJ AF: 0.000818

Gnomad EAS AF: 0.00129

Gnomad SAS AF: 0.000600

Gnomad FIN AF: 0.000816

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00299

Gnomad OTH AF: 0.00145

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: AS_VQSR AF: 0.00167 AC: 166 AN: 99158 Hom.: 0 Cov.: 28 AF XY: 0.00153 AC XY: 74 AN XY: 48472

African (AFR) AF: 0.000597 AC: 17 AN: 28468

American (AMR) AF: 0.000649 AC: 7 AN: 10784

Ashkenazi Jewish (ASJ) AF: 0.000818 AC: 2 AN: 2446

East Asian (EAS) AF: 0.00129 AC: 5 AN: 3868

South Asian (SAS) AF: 0.000601 AC: 2 AN: 3326

European-Finnish (FIN) AF: 0.000816 AC: 5 AN: 6126

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 182

European-Non Finnish (NFE) AF: 0.00299 AC: 126 AN: 42086

Other (OTH) AF: 0.00143 AC: 2 AN: 1400

Alfa AF: 0.0375 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.56
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: rs3885584;

hg19: chr22-46542403;