chr4-107408461-A-G

Variant names:

• chr4-107408461-A-G
• rs203202

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 0.409 in 151,944 control chromosomes in the GnomAD database, including 12,746 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 0.41 (12746 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 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: 0.409 AC: 62121 AN: 151826 Hom.: 12716 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.409 AC: 62203 AN: 151944 Hom.: 12746 Cov.: 31 AF XY: 0.410 AC XY: 30436 AN XY: 74296

African (AFR) AF: 0.443 AC: 18345 AN: 41430

American (AMR) AF: 0.450 AC: 6865 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.375 AC: 1936 AN: 5158

South Asian (SAS) AF: 0.385 AC: 1851 AN: 4814

European-Finnish (FIN) AF: 0.378 AC: 4000 AN: 10578

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26552 AN: 67922

Other (OTH) AF: 0.387 AC: 818 AN: 2112

Alfa AF: 0.398 Hom.: 20871

Bravo AF: 0.418

Asia WGS AF: 0.390 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs203202; hg19: chr4-108329618;