4-180338224-C-T

Variant names:

• chr4-180338224-C-T
• rs4861849

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 0.105 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.207 AC: 8602 AN: 41456

American (AMR) AF: 0.0782 AC: 1193 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3468

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5170

South Asian (SAS) AF: 0.0729 AC: 351 AN: 4816

European-Finnish (FIN) AF: 0.0475 AC: 503 AN: 10586

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4475 AN: 68006

Other (OTH) AF: 0.115 AC: 243 AN: 2114

Alfa AF: 0.0783 Hom.: 974

Bravo AF: 0.112

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4861849; hg19: chr4-181259377;