rs1423297

Variant names:

• chr5-28767880-G-A
• rs1423297
• ENST00000653909.1:n.321+41076C>T

Variant summary

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

The ENST00000653909.1(ENSG00000250453):​n.321+41076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,906 control chromosomes in the GnomAD database, including 24,083 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 0.56 (24083 hom., cov: 32)
• Consequence: ENSG00000250453 ENST00000653909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 4 publications found

Genes affected

ENSG00000250453 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250453	ENST00000653909.1		n.321+41076C>T		intron	N/A
	ENSG00000250453	ENST00000660682.1		n.336+41076C>T		intron	N/A
	ENSG00000250453	ENST00000849332.1		n.340+41076C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84647 AN: 151788 Hom.: 24088 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.557 AC: 84672 AN: 151906 Hom.: 24083 Cov.: 32 AF XY: 0.563 AC XY: 41779 AN XY: 74238

African (AFR) AF: 0.449 AC: 18573 AN: 41398

American (AMR) AF: 0.620 AC: 9468 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2306 AN: 3468

East Asian (EAS) AF: 0.641 AC: 3298 AN: 5142

South Asian (SAS) AF: 0.611 AC: 2946 AN: 4818

European-Finnish (FIN) AF: 0.600 AC: 6329 AN: 10550

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39805 AN: 67948

Other (OTH) AF: 0.578 AC: 1218 AN: 2108

Alfa AF: 0.584 Hom.: 21477

Bravo AF: 0.557

Asia WGS AF: 0.584 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.086
DANN	Benign	0.45
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1423297; hg19: chr5-28767987;