rs2472299

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;