chr15-73854903-A-G

Variant names:

• chr15-73854903-A-G
• rs1823718

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 0.405 in 152,018 control chromosomes in the GnomAD database, including 13,720 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 0.40 (13720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.405 AC: 61549 AN: 151898 Hom.: 13719 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.0428

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.405 AC: 61560 AN: 152018 Hom.: 13720 Cov.: 32 AF XY: 0.401 AC XY: 29839 AN XY: 74332

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.0429

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.429

Alfa AF: 0.484 Hom.: 37398

Bravo AF: 0.399

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1823718; hg19: chr15-74147244;