ENST00000424958.2:n.1752G>C

Variant names:

• chr4-121766336-G-C
• rs4833772
• ENST00000424958.2:n.1752G>C

Variant summary

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

The ENST00000424958.2(PP12613):​n.1752G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 453,606 control chromosomes in the GnomAD database, including 68,983 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 0.57 (25243 hom., cov: 32)
  • Exomes 𝑓: 0.53 (43740 hom.)
• Consequence: PP12613 ENST00000424958.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 11 publications found

Genes affected

PP12613 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (REVEL=0.033).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424958.2. 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
	PP12613	NR_024365.1		n.1752G>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PP12613	ENST00000424958.2	TSL:6	n.1752G>C		non_coding_transcript_exon	Exon 1 of 1
	PP12613	ENST00000746424.1		n.240+917G>C		intron	N/A
	PP12613	ENST00000746425.1		n.238+917G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86388 AN: 151860 Hom.: 25217 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.557

GnomAD2 exomes AF: 0.558 AC: 71439 AN: 128006 AF XY: 0.556

Gnomad AFR exome AF: 0.705

Gnomad AMR exome AF: 0.597

Gnomad ASJ exome AF: 0.541

Gnomad EAS exome AF: 0.671

Gnomad FIN exome AF: 0.467

Gnomad NFE exome AF: 0.502

Gnomad OTH exome AF: 0.543

GnomAD4 exome AF: 0.534 AC: 161004 AN: 301628 Hom.: 43740 Cov.: 0 AF XY: 0.536 AC XY: 92113 AN XY: 171882

African (AFR) AF: 0.695 AC: 5944 AN: 8554

American (AMR) AF: 0.596 AC: 16239 AN: 27264

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 5721 AN: 10744

East Asian (EAS) AF: 0.671 AC: 6169 AN: 9200

South Asian (SAS) AF: 0.577 AC: 34395 AN: 59570

European-Finnish (FIN) AF: 0.478 AC: 5895 AN: 12342

Middle Eastern (MID) AF: 0.547 AC: 765 AN: 1398

European-Non Finnish (NFE) AF: 0.494 AC: 78232 AN: 158520

Other (OTH) AF: 0.545 AC: 7644 AN: 14036

GnomAD4 genome AF: 0.569 AC: 86468 AN: 151978 Hom.: 25243 Cov.: 32 AF XY: 0.569 AC XY: 42282 AN XY: 74290

African (AFR) AF: 0.696 AC: 28839 AN: 41438

American (AMR) AF: 0.576 AC: 8801 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1877 AN: 3466

East Asian (EAS) AF: 0.665 AC: 3433 AN: 5164

South Asian (SAS) AF: 0.590 AC: 2848 AN: 4824

European-Finnish (FIN) AF: 0.471 AC: 4966 AN: 10548

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33943 AN: 67960

Other (OTH) AF: 0.556 AC: 1171 AN: 2106

Alfa AF: 0.519 Hom.: 3699

Bravo AF: 0.582

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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: rs4833772;

hg19: chr4-122687491;