chr15-78420357-A-C

Variant names:

• chr15-78420357-A-C
• rs4887053

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 0.788 in 152,090 control chromosomes in the GnomAD database, including 47,498 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 0.79 (47498 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.788 AC: 119736 AN: 151972 Hom.: 47447 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.788 AC: 119841 AN: 152090 Hom.: 47498 Cov.: 31 AF XY: 0.785 AC XY: 58340 AN XY: 74348

African (AFR) AF: 0.848 AC: 35206 AN: 41500

American (AMR) AF: 0.658 AC: 10044 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2750 AN: 3472

East Asian (EAS) AF: 0.734 AC: 3775 AN: 5146

South Asian (SAS) AF: 0.754 AC: 3637 AN: 4824

European-Finnish (FIN) AF: 0.751 AC: 7945 AN: 10580

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53870 AN: 67988

Other (OTH) AF: 0.771 AC: 1628 AN: 2112

Alfa AF: 0.786 Hom.: 145098

Bravo AF: 0.786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.50
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs4887053; hg19: chr15-78712699;