10-100372778-C-T

Variant names:

• chr10-100372778-C-T
• rs569910
• ENST00000693438.2:n.616G>A

Variant summary

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

The ENST00000693438.2(ENSG00000289301):​n.616G>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 0.292 in 152,000 control chromosomes in the GnomAD database, including 8,963 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 0.29 (8963 hom., cov: 32)
• Consequence: ENSG00000289301 ENST00000693438.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

ENSG00000289301 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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
ENSG00000289301	ENST00000693438.2	n.616G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44270 AN: 151882 Hom.: 8922 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.292 AC: 44353 AN: 152000 Hom.: 8963 Cov.: 32 AF XY: 0.289 AC XY: 21471 AN XY: 74288

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.243

Alfa AF: 0.207 Hom.: 1871

Bravo AF: 0.299

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs569910; hg19: chr10-102132535;