4-127048900-A-G

Variant names:

• chr4-127048900-A-G
• rs17012036
• ENST00000506852.1:n.144-4966T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000506852.1(ENSG00000250945):​n.144-4966T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,124 control chromosomes in the GnomAD database, including 294 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 0.020 (294 hom., cov: 32)
• Consequence: ENSG00000250945 ENST00000506852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 3 publications found

Genes affected

ENSG00000250945 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506852.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250945	ENST00000506852.1	TSL:3	n.144-4966T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3112 AN: 152006 Hom.: 296 Cov.: 32

Gnomad AFR AF: 0.00454

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.00387

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00100

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0204 AC: 3110 AN: 152124 Hom.: 294 Cov.: 32 AF XY: 0.0238 AC XY: 1772 AN XY: 74348

African (AFR) AF: 0.00452 AC: 188 AN: 41564

American (AMR) AF: 0.0769 AC: 1174 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1523 AN: 5132

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4824

European-Finnish (FIN) AF: 0.00387 AC: 41 AN: 10598

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00100 AC: 68 AN: 67960

Other (OTH) AF: 0.0142 AC: 30 AN: 2110

Alfa AF: 0.00600 Hom.: 23

Bravo AF: 0.0265

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17012036; hg19: chr4-127970055;