4-106602743-C-T

Variant names:

• chr4-106602743-C-T
• rs17036834
• ENST00000650850.1:n.102-17633C>T

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.102-17633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.071 in 151,852 control chromosomes in the GnomAD database, including 505 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 0.071 (505 hom., cov: 31)
• Consequence: ENSG00000286147 ENST00000650850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 3 publications found

Genes affected

ENSG00000286147 (HGNC:58864):

LOC105377356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650850.1. 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
	ENSG00000286147	ENST00000650850.1		n.102-17633C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10770 AN: 151734 Hom.: 504 Cov.: 31

Gnomad AFR AF: 0.0732

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0654

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0710 AC: 10784 AN: 151852 Hom.: 505 Cov.: 31 AF XY: 0.0743 AC XY: 5513 AN XY: 74202

African (AFR) AF: 0.0731 AC: 3026 AN: 41418

American (AMR) AF: 0.123 AC: 1866 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3468

East Asian (EAS) AF: 0.104 AC: 538 AN: 5162

South Asian (SAS) AF: 0.0658 AC: 317 AN: 4816

European-Finnish (FIN) AF: 0.0917 AC: 963 AN: 10496

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0551 AC: 3742 AN: 67952

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0581 Hom.: 221

Bravo AF: 0.0746

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.44
PhyloP100		-0.31

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: rs17036834;

hg19: chr4-107523900;