chr1-4266308-G-A

Variant names:

• chr1-4266308-G-A
• rs2411738

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 0.399 in 152,074 control chromosomes in the GnomAD database, including 13,877 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 0.40 (13877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.53
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 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: 0.399 AC: 60569 AN: 151956 Hom.: 13870 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.399 AC: 60602 AN: 152074 Hom.: 13877 Cov.: 32 AF XY: 0.400 AC XY: 29737 AN XY: 74348

African (AFR) AF: 0.166 AC: 6901 AN: 41500

American (AMR) AF: 0.507 AC: 7748 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1566 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1163 AN: 5150

South Asian (SAS) AF: 0.505 AC: 2426 AN: 4808

European-Finnish (FIN) AF: 0.490 AC: 5185 AN: 10574

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34241 AN: 67968

Other (OTH) AF: 0.397 AC: 839 AN: 2114

Alfa AF: 0.468 Hom.: 10115

Bravo AF: 0.384

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.25
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs2411738; hg19: chr1-4326368;