4-166422787-A-G

Variant names:

• chr4-166422787-A-G
• rs17635075
• ENST00000514134.1:n.206-33358T>C

Variant summary

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

The ENST00000514134.1(ENSG00000249675):​n.206-33358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.094 in 152,200 control chromosomes in the GnomAD database, including 940 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 0.094 (940 hom., cov: 32)
• Consequence: ENSG00000249675 ENST00000514134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 4 publications found

Genes affected

ENSG00000249675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514134.1. 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
	ENSG00000249675	ENST00000514134.1	TSL:3	n.206-33358T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14288 AN: 152082 Hom.: 935 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0940 AC: 14310 AN: 152200 Hom.: 940 Cov.: 32 AF XY: 0.0952 AC XY: 7084 AN XY: 74400

African (AFR) AF: 0.147 AC: 6107 AN: 41510

American (AMR) AF: 0.0753 AC: 1152 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1144 AN: 5174

South Asian (SAS) AF: 0.187 AC: 903 AN: 4820

European-Finnish (FIN) AF: 0.0230 AC: 244 AN: 10604

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3742 AN: 68012

Other (OTH) AF: 0.119 AC: 251 AN: 2110

Alfa AF: 0.0928 Hom.: 656

Bravo AF: 0.101

Asia WGS AF: 0.204 AC: 708 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism

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: rs17635075;

hg19: chr4-167343939;