rs4561414

chr15-95629095-G-A

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 0.109 in 152,110 control chromosomes in the GnomAD database, including 1,076 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 0.11 (1076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16617 AN: 151992 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0778

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.109 AC: 16637 AN: 152110 Hom.: 1076 Cov.: 32 AF XY: 0.110 AC XY: 8152 AN XY: 74358

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.0863

Gnomad4 FIN AF: 0.0498

Gnomad4 NFE AF: 0.0778

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0850 Hom.: 771

Bravo AF: 0.120

Asia WGS AF: 0.102 AC: 354 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	14
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4561414; hg19: chr15-96172324;