rs4118325

Variant names:

• chr1-107035210-G-A
• rs4118325

Your query was ambiguous. Multiple possible variants found:

• chr1-107035210-G-A
• chr1-107035210-G-T

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 0.21 in 151,890 control chromosomes in the GnomAD database, including 3,386 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 0.21 (3386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 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: 0.210 AC: 31906 AN: 151772 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.210 AC: 31933 AN: 151890 Hom.: 3386 Cov.: 32 AF XY: 0.213 AC XY: 15817 AN XY: 74220

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.216

Alfa AF: 0.184 Hom.: 5730

Bravo AF: 0.203

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4118325; hg19: chr1-107577832;