rs1423297

chr5-28767880-G-A

Variant summary

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

The ENST00000653909.1(ENSG00000250453):n.321+41076C>T 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 0.557 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: ENST00000653909.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653909.1	n.321+41076C>T		intron_variant, non_coding_transcript_variant
	ENST00000660682.1	n.336+41076C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.578

Alfa AF: 0.586 Hom.: 17999

Bravo AF: 0.557

Asia WGS AF: 0.584 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.086
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1423297; hg19: chr5-28767987;