rs2414351

Variant names:

• chr15-54667075-C-G
• rs2414351

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 0.737 in 152,160 control chromosomes in the GnomAD database, including 41,434 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 0.74 (41434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112027 AN: 152042 Hom.: 41392 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.737 AC: 112122 AN: 152160 Hom.: 41434 Cov.: 32 AF XY: 0.738 AC XY: 54899 AN XY: 74408

African (AFR) AF: 0.692 AC: 28741 AN: 41512

American (AMR) AF: 0.744 AC: 11364 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2857 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3804 AN: 5160

South Asian (SAS) AF: 0.773 AC: 3728 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8226 AN: 10610

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 51010 AN: 67986

Other (OTH) AF: 0.727 AC: 1535 AN: 2112

Alfa AF: 0.744 Hom.: 5223

Bravo AF: 0.724

Asia WGS AF: 0.758 AC: 2641 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	0.21
DANN	Benign	0.60
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2414351; hg19: chr15-54959273;