4-180203097-C-A

Variant names:

• chr4-180203097-C-A
• rs1868056

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.438 AC: 18112 AN: 41340

American (AMR) AF: 0.475 AC: 7229 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3466

East Asian (EAS) AF: 0.749 AC: 3865 AN: 5158

South Asian (SAS) AF: 0.572 AC: 2749 AN: 4802

European-Finnish (FIN) AF: 0.409 AC: 4296 AN: 10496

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26776 AN: 67948

Other (OTH) AF: 0.411 AC: 865 AN: 2104

Alfa AF: 0.409 Hom.: 35812

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1868056; hg19: chr4-181124250;