rs2413583

chr22-39263768-C-T

Variant summary

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

The ENST00000641859.1(ENSG00000284633):n.110-12808C>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 0.189 in 152,142 control chromosomes in the GnomAD database, including 3,144 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 0.19 (3144 hom., cov: 32)
• Consequence: ENST00000641859.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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
	ENST00000641859.1	n.110-12808C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28771 AN: 152024 Hom.: 3133 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.189 AC: 28818 AN: 152142 Hom.: 3144 Cov.: 32 AF XY: 0.183 AC XY: 13634 AN XY: 74358

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.185

Alfa AF: 0.169 Hom.: 5287

Bravo AF: 0.195

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.17
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2413583; hg19: chr22-39659773;