rs17274722

chr21-14926209-C-T

Variant summary

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

The ENST00000430391.1(ENSG00000235277):n.239+7437C>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 0.0662 in 152,164 control chromosomes in the GnomAD database, including 432 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 0.066 (432 hom., cov: 32)
• Consequence: ENST00000430391.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0991 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
	ENST00000430391.1	n.239+7437C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10072 AN: 152046 Hom.: 432 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0787

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

GnomAD4 genome AF: 0.0662 AC: 10077 AN: 152164 Hom.: 432 Cov.: 32 AF XY: 0.0651 AC XY: 4842 AN XY: 74382

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0478

Gnomad4 FIN AF: 0.0639

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.0779

Alfa AF: 0.0875 Hom.: 181

Bravo AF: 0.0705

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	15
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17274722; hg19: chr21-16298530;