rs2433320

Variant names:

• chr4-94449654-G-A
• rs2433320

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 0.365 in 151,490 control chromosomes in the GnomAD database, including 10,674 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 0.36 (10674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 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: 0.365 AC: 55209 AN: 151370 Hom.: 10671 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.365 AC: 55233 AN: 151490 Hom.: 10674 Cov.: 32 AF XY: 0.358 AC XY: 26511 AN XY: 74028

African (AFR) AF: 0.274 AC: 11239 AN: 41036

American (AMR) AF: 0.328 AC: 5010 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3472

East Asian (EAS) AF: 0.185 AC: 956 AN: 5174

South Asian (SAS) AF: 0.208 AC: 998 AN: 4802

European-Finnish (FIN) AF: 0.400 AC: 4198 AN: 10502

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29981 AN: 67942

Other (OTH) AF: 0.406 AC: 854 AN: 2102

Alfa AF: 0.408 Hom.: 58816

Bravo AF: 0.352

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.32
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs2433320; hg19: chr4-95370805;