rs9305545

Positions:

• chr21-34223520-A-G

Variant summary

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

The ENST00000427022.1(ENSG00000214955):​n.311+7980A>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 0.152 in 152,250 control chromosomes in the GnomAD database, including 1,910 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 0.15 (1910 hom., cov: 32)
• Consequence: ENST00000427022.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 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
	ENST00000427022.1	n.311+7980A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23152 AN: 152132 Hom.: 1910 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.152 AC: 23165 AN: 152250 Hom.: 1910 Cov.: 32 AF XY: 0.151 AC XY: 11222 AN XY: 74440

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0557

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.143

Alfa AF: 0.153 Hom.: 1872

Bravo AF: 0.148

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.92
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9305545; hg19: chr21-35595821;