rs10825992

Positions:

• chr10-57188447-T-G

Variant summary

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

The ENST00000690550.1(ENSG00000289158):​n.96+34165A>C 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 0.437 in 151,340 control chromosomes in the GnomAD database, including 17,168 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 0.44 (17168 hom., cov: 31)
• Consequence: ENST00000690550.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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
	ENST00000690550.1	n.96+34165A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66072 AN: 151220 Hom.: 17147 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.437 AC: 66142 AN: 151340 Hom.: 17168 Cov.: 31 AF XY: 0.431 AC XY: 31862 AN XY: 73964

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.418

Alfa AF: 0.362 Hom.: 5653

Bravo AF: 0.456

Asia WGS AF: 0.279 AC: 965 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10825992; hg19: chr10-58948207;