chr10-57146289-C-T

Variant names:

• chr10-57146289-C-T
• rs7906620
• ENST00000690550.1:n.97-37538G>A

Variant summary

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

The ENST00000690550.1(ENSG00000289158):​n.97-37538G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,984 control chromosomes in the GnomAD database, including 5,992 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 0.26 (5992 hom., cov: 32)
• Consequence: ENSG00000289158 ENST00000690550.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

ENSG00000289158 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289158	ENST00000690550.1	n.97-37538G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39916 AN: 151864 Hom.: 5982 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00254

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.263 AC: 39959 AN: 151984 Hom.: 5992 Cov.: 32 AF XY: 0.260 AC XY: 19303 AN XY: 74296

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00255

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.260

Alfa AF: 0.229 Hom.: 760

Bravo AF: 0.266

Asia WGS AF: 0.101 AC: 351 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7906620; hg19: chr10-58906049;