rs923976

Positions:

• chr1-233862321-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655369.1(ENSG00000286666):​n.222+2828A>G variant causes a intron, non coding transcript 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: ENST00000655369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000655369.1	n.222+2828A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.381

Alfa AF: 0.474 Hom.: 23145

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs923976; hg19: chr1-233998067;