rs1506005

chr21-23085620-T-Cchr21-23085620-T-A

Variant summary

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

The ENST00000421604.1(ENSG00000230972):n.297+17584T>C 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 0.0769 in 152,046 control chromosomes in the GnomAD database, including 656 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 0.077 (656 hom., cov: 32)
• Consequence: ENST00000421604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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
	ENST00000421604.1	n.297+17584T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11691 AN: 151928 Hom.: 654 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0341

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.0769 AC: 11697 AN: 152046 Hom.: 656 Cov.: 32 AF XY: 0.0749 AC XY: 5570 AN XY: 74328

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0333

Gnomad4 FIN AF: 0.0183

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0820

Alfa AF: 0.0576 Hom.: 43

Bravo AF: 0.0849

Asia WGS AF: 0.0740 AC: 256 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1506005; hg19: chr21-24457942;