15-73854903-A-G

Variant names:

• chr15-73854903-A-G
• rs1823718

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 0.405 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.250 AC: 10354 AN: 41470

American (AMR) AF: 0.468 AC: 7134 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1979 AN: 3472

East Asian (EAS) AF: 0.0429 AC: 222 AN: 5178

South Asian (SAS) AF: 0.335 AC: 1609 AN: 4810

European-Finnish (FIN) AF: 0.460 AC: 4856 AN: 10568

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33921 AN: 67952

Other (OTH) AF: 0.429 AC: 906 AN: 2110

Alfa AF: 0.472 Hom.: 54415

Bravo AF: 0.399

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.45
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1823718; hg19: chr15-74147244;