rs4800417

Variant names:

• chr18-22564362-C-T
• rs4800417
• ENST00000731318.1:n.309-18676C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000731318.1(ENSG00000295614):​n.309-18676C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,954 control chromosomes in the GnomAD database, including 6,318 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 0.28 (6318 hom., cov: 32)
• Consequence: ENSG00000295614 ENST00000731318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 4 publications found

Genes affected

ENSG00000295614 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731318.1. 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
	ENSG00000295614	ENST00000731318.1		n.309-18676C>T		intron	N/A
	ENSG00000295614	ENST00000731322.1		n.277-241C>T		intron	N/A
	ENSG00000295614	ENST00000731317.1		n.*166C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41932 AN: 151836 Hom.: 6311 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.276 AC: 41960 AN: 151954 Hom.: 6318 Cov.: 32 AF XY: 0.279 AC XY: 20752 AN XY: 74270

African (AFR) AF: 0.176 AC: 7284 AN: 41452

American (AMR) AF: 0.435 AC: 6643 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.191 AC: 984 AN: 5152

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4812

European-Finnish (FIN) AF: 0.307 AC: 3230 AN: 10536

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20517 AN: 67960

Other (OTH) AF: 0.296 AC: 625 AN: 2112

Alfa AF: 0.283 Hom.: 787

Bravo AF: 0.283

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.75
PhyloP100		0.11

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: rs4800417;

hg19: chr18-20144325;