chr4-121766336-G-C

Position:

• chr4-121766336-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024365.1(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 NR_024365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

Genes affected

PP12613 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PP12613	NR_024365.1	n.1752G>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PP12613	ENST00000424958.2	n.1752G>C		non_coding_transcript_exon_variant	1/1

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

GnomAD3 exomes AF: 0.558 AC: 71439 AN: 128006 Hom.: 20265 AF XY: 0.556 AC XY: 38975 AN XY: 70090

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 SAS exome AF: 0.574

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

Gnomad4 AFR exome AF: 0.695

Gnomad4 AMR exome AF: 0.596

Gnomad4 ASJ exome AF: 0.532

Gnomad4 EAS exome AF: 0.671

Gnomad4 SAS exome AF: 0.577

Gnomad4 FIN exome AF: 0.478

Gnomad4 NFE exome AF: 0.494

Gnomad4 OTH exome AF: 0.545

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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.556

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833772; hg19: chr4-122687491;