4-171483944-T-G

Variant names:

• chr4-171483944-T-G
• rs4144862
• ENST00000782802.1:n.164-6073T>G

Variant summary

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

The ENST00000782802.1(ENSG00000301909):​n.164-6073T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,802 control chromosomes in the GnomAD database, including 19,251 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 0.41 (19251 hom., cov: 32)
• Consequence: ENSG00000301909 ENST00000782802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 3 publications found

Genes affected

ENSG00000301909 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782802.1. 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
	ENSG00000301909	ENST00000782802.1		n.164-6073T>G		intron	N/A
	ENSG00000301909	ENST00000782803.1		n.136-6073T>G		intron	N/A
	ENSG00000301909	ENST00000782804.1		n.91+8587T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62566 AN: 151684 Hom.: 19192 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.413 AC: 62682 AN: 151802 Hom.: 19251 Cov.: 32 AF XY: 0.412 AC XY: 30539 AN XY: 74208

African (AFR) AF: 0.855 AC: 35444 AN: 41454

American (AMR) AF: 0.370 AC: 5629 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 858 AN: 3464

East Asian (EAS) AF: 0.554 AC: 2856 AN: 5152

South Asian (SAS) AF: 0.363 AC: 1745 AN: 4808

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10590

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13660 AN: 67788

Other (OTH) AF: 0.368 AC: 776 AN: 2110

Alfa AF: 0.230 Hom.: 9195

Bravo AF: 0.452

Asia WGS AF: 0.482 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.54
PhyloP100		-0.50

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: rs4144862;

hg19: chr4-172405095;