rs9815663

Variant names:

• chr3-3573203-C-T
• rs9815663
• ENST00000420000.6:n.200+53541G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420000.6(ENSG00000223727):​n.200+53541G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,070 control chromosomes in the GnomAD database, including 3,541 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 0.21 (3541 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 16 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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
ENSG00000223727	ENST00000420000.6	n.200+53541G>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32501 AN: 151952 Hom.: 3535 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.214 AC: 32537 AN: 152070 Hom.: 3541 Cov.: 32 AF XY: 0.212 AC XY: 15776 AN XY: 74336

African (AFR) AF: 0.251 AC: 10393 AN: 41458

American (AMR) AF: 0.173 AC: 2638 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 685 AN: 3472

East Asian (EAS) AF: 0.189 AC: 976 AN: 5170

South Asian (SAS) AF: 0.174 AC: 836 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2506 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13759 AN: 67988

Other (OTH) AF: 0.203 AC: 428 AN: 2110

Alfa AF: 0.202 Hom.: 10781

Bravo AF: 0.210

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.95
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs9815663; hg19: chr3-3614887;