chr4-180203097-C-A

Position:

• chr4-180203097-C-A

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 0.432 in 151,746 control chromosomes in the GnomAD database, including 14,592 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 0.43 (14592 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65481 AN: 151628 Hom.: 14589 Cov.: 31

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.432 AC: 65535 AN: 151746 Hom.: 14592 Cov.: 31 AF XY: 0.437 AC XY: 32372 AN XY: 74096

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.411

Alfa AF: 0.395 Hom.: 12154

Bravo AF: 0.436

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1868056; hg19: chr4-181124250;