chr4-23786718-T-C

Position:

• chr4-23786718-T-C

Variant summary

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

The variant allele was found at a frequency of 0.385 in 151,658 control chromosomes in the GnomAD database, including 11,476 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 0.38 (11476 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23786718T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPARGC1A	ENST00000509702.5	n.2433+9108A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58251 AN: 151540 Hom.: 11456 Cov.: 30

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.385 AC: 58328 AN: 151658 Hom.: 11476 Cov.: 30 AF XY: 0.388 AC XY: 28725 AN XY: 74108

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.374

Alfa AF: 0.336 Hom.: 18143

Bravo AF: 0.378

Asia WGS AF: 0.398 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2970882; hg19: chr4-23788341;