rs2472300

Variant names:

• chr15-74741568-A-G
• rs2472300

Your query was ambiguous. Multiple possible variants found:

• chr15-74741568-A-G
• chr15-74741568-A-T

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 0.673 in 151,984 control chromosomes in the GnomAD database, including 34,761 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 0.67 (34761 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 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: 0.673 AC: 102235 AN: 151866 Hom.: 34722 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.673 AC: 102332 AN: 151984 Hom.: 34761 Cov.: 31 AF XY: 0.669 AC XY: 49689 AN XY: 74274

African (AFR) AF: 0.606 AC: 25081 AN: 41416

American (AMR) AF: 0.708 AC: 10808 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2457 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3385 AN: 5172

South Asian (SAS) AF: 0.570 AC: 2741 AN: 4806

European-Finnish (FIN) AF: 0.688 AC: 7262 AN: 10562

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48390 AN: 67978

Other (OTH) AF: 0.670 AC: 1413 AN: 2108

Alfa AF: 0.701 Hom.: 148028

Bravo AF: 0.677

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.46
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs2472300; hg19: chr15-75033909;