rs2472299

Variant names:

• chr15-74741059-A-G
• rs2472299

Your query was ambiguous. Multiple possible variants found:

• chr15-74741059-A-G
• chr15-74741059-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.675 in 152,040 control chromosomes in the GnomAD database, including 34,944 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 0.68 (34944 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.675 AC: 102570 AN: 151922 Hom.: 34905 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.675 AC: 102669 AN: 152040 Hom.: 34944 Cov.: 31 AF XY: 0.671 AC XY: 49865 AN XY: 74312

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.673

Alfa AF: 0.701 Hom.: 80750

Bravo AF: 0.679

Asia WGS AF: 0.665 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2472299; hg19: chr15-75033400;