rs10483181

Positions:

• chr22-34719131-T-C

Variant summary

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

The ENST00000440858.1(ENSG00000237316):​n.65-5158A>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 0.028 in 152,216 control chromosomes in the GnomAD database, including 92 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 0.028 (92 hom., cov: 33)
• Consequence: ENST00000440858.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.103 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
	ENST00000440858.1	n.65-5158A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0280 AC: 4262 AN: 152098 Hom.: 92 Cov.: 33

Gnomad AFR AF: 0.00899

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0280 AC: 4261 AN: 152216 Hom.: 92 Cov.: 33 AF XY: 0.0302 AC XY: 2247 AN XY: 74450

Gnomad4 AFR AF: 0.00893

Gnomad4 AMR AF: 0.0556

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0232

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0235 Hom.: 7

Bravo AF: 0.0286

Asia WGS AF: 0.0580 AC: 201 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483181; hg19: chr22-35115122;