rs923976

Variant names:

• chr1-233862321-T-C
• rs923976
• ENST00000655369.1:n.222+2828A>G

Variant summary

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

The ENST00000655369.1(ENSG00000286666):​n.222+2828A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,762 control chromosomes in the GnomAD database, including 14,504 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 0.43 (14504 hom., cov: 30)
• Consequence: ENSG00000286666 ENST00000655369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807
• Publications: 1 publications found

Genes affected

ENSG00000286666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 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
ENSG00000286666	ENST00000655369.1	n.222+2828A>G		intron_variant	Intron 1 of 1
ENSG00000306050	ENST00000814968.1	n.248+6109A>G		intron_variant	Intron 1 of 4
ENSG00000286666	ENST00000815093.1	n.247-2510A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64892 AN: 151644 Hom.: 14499 Cov.: 30

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.428 AC: 64901 AN: 151762 Hom.: 14504 Cov.: 30 AF XY: 0.426 AC XY: 31620 AN XY: 74148

African (AFR) AF: 0.316 AC: 13073 AN: 41388

American (AMR) AF: 0.336 AC: 5113 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1660 AN: 3464

East Asian (EAS) AF: 0.299 AC: 1537 AN: 5136

South Asian (SAS) AF: 0.346 AC: 1654 AN: 4784

European-Finnish (FIN) AF: 0.560 AC: 5889 AN: 10522

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34633 AN: 67922

Other (OTH) AF: 0.381 AC: 801 AN: 2104

Alfa AF: 0.469 Hom.: 28615

Bravo AF: 0.404

Asia WGS AF: 0.279 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs923976; hg19: chr1-233998067;