chr1-4122725-G-T

Variant names:

• chr1-4122725-G-T
• rs4400585

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 0.874 in 152,248 control chromosomes in the GnomAD database, including 58,377 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 0.87 (58377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.873 AC: 132873 AN: 152128 Hom.: 58316 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.874 AC: 132993 AN: 152248 Hom.: 58377 Cov.: 32 AF XY: 0.878 AC XY: 65376 AN XY: 74436

African (AFR) AF: 0.938 AC: 38985 AN: 41550

American (AMR) AF: 0.868 AC: 13274 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2839 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5153 AN: 5168

South Asian (SAS) AF: 0.950 AC: 4588 AN: 4828

European-Finnish (FIN) AF: 0.885 AC: 9386 AN: 10606

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55985 AN: 68008

Other (OTH) AF: 0.844 AC: 1786 AN: 2116

Alfa AF: 0.854 Hom.: 12047

Bravo AF: 0.873

Asia WGS AF: 0.969 AC: 3370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs4400585; hg19: chr1-4182785;