10-78706883-A-G

Variant names:

• chr10-78706883-A-G
• rs650389
• ENST00000764443.1:n.444+37215T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000764443.1(ENSG00000228683):​n.444+37215T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,190 control chromosomes in the GnomAD database, including 3,290 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 0.18 (3290 hom., cov: 32)
• Consequence: ENSG00000228683 ENST00000764443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.77
• Publications: 3 publications found

Genes affected

ENSG00000228683 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378379	XR_946100.2	n.446+37215T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228683	ENST00000764443.1	n.444+37215T>C		intron_variant	Intron 1 of 3
ENSG00000228683	ENST00000764444.1	n.425+37215T>C		intron_variant	Intron 1 of 2
ENSG00000228683	ENST00000764445.1	n.76+37215T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27883 AN: 152072 Hom.: 3295 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.183 AC: 27864 AN: 152190 Hom.: 3290 Cov.: 32 AF XY: 0.179 AC XY: 13308 AN XY: 74402

African (AFR) AF: 0.0509 AC: 2117 AN: 41558

American (AMR) AF: 0.169 AC: 2581 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2281 AN: 5152

South Asian (SAS) AF: 0.284 AC: 1370 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1354 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17026 AN: 67996

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.221 Hom.: 11574

Bravo AF: 0.177

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	21
DANN	Benign	0.81
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs650389; hg19: chr10-80466640;