rs4653436

Variant names:

• chr1-225807509-G-A
• rs4653436

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 0.257 in 151,928 control chromosomes in the GnomAD database, including 5,517 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 0.26 (5517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38996 AN: 151810 Hom.: 5514 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.257 AC: 39014 AN: 151928 Hom.: 5517 Cov.: 32 AF XY: 0.258 AC XY: 19174 AN XY: 74224

African (AFR) AF: 0.141 AC: 5844 AN: 41462

American (AMR) AF: 0.274 AC: 4179 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5152

South Asian (SAS) AF: 0.238 AC: 1145 AN: 4820

European-Finnish (FIN) AF: 0.340 AC: 3568 AN: 10508

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21386 AN: 67954

Other (OTH) AF: 0.270 AC: 571 AN: 2112

Alfa AF: 0.293 Hom.: 22104

Bravo AF: 0.244

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.83
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs4653436; hg19: chr1-225995211;