4-180338224-C-T

Variant names:

• chr4-180338224-C-T
• rs4861849

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 0.105 in 152,070 control chromosomes in the GnomAD database, including 1,279 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 0.11 (1279 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 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: 0.105 AC: 15936 AN: 151952 Hom.: 1272 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0784

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.105 AC: 15972 AN: 152070 Hom.: 1279 Cov.: 33 AF XY: 0.103 AC XY: 7681 AN XY: 74336

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0782

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.0658

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0733 Hom.: 648

Bravo AF: 0.112

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4861849; hg19: chr4-181259377;