rs570844

Positions:

• chr10-100372886-C-T

Variant summary

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

The ENST00000693438.2(ENSG00000289301):​n.508G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 152,280 control chromosomes in the GnomAD database, including 231 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 0.039 (231 hom., cov: 31)
• Consequence: ENST00000693438.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 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
	ENST00000693438.2	n.508G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5913 AN: 152162 Hom.: 232 Cov.: 31

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0248

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00645

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0389 AC: 5928 AN: 152280 Hom.: 231 Cov.: 31 AF XY: 0.0424 AC XY: 3159 AN XY: 74464

Gnomad4 AFR AF: 0.0823

Gnomad4 AMR AF: 0.0249

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.0635

Gnomad4 NFE AF: 0.00645

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0148 Hom.: 48

Bravo AF: 0.0366

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs570844; hg19: chr10-102132643;