10-16553397-A-G

Variant names:

• chr10-16553397-A-G
• rs7084722
• ENST00000777741.1:n.204+25646A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000777741.1(ENSG00000287925):​n.204+25646A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,090 control chromosomes in the GnomAD database, including 12,581 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 0.38 (12581 hom., cov: 32)
• Consequence: ENSG00000287925 ENST00000777741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 9 publications found

Genes affected

ENSG00000287925 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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
ENSG00000287925	ENST00000777741.1	n.204+25646A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57701 AN: 151972 Hom.: 12587 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.379 AC: 57710 AN: 152090 Hom.: 12581 Cov.: 32 AF XY: 0.390 AC XY: 29002 AN XY: 74338

African (AFR) AF: 0.164 AC: 6789 AN: 41496

American (AMR) AF: 0.405 AC: 6184 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2988 AN: 5154

South Asian (SAS) AF: 0.496 AC: 2396 AN: 4826

European-Finnish (FIN) AF: 0.618 AC: 6536 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30111 AN: 67972

Other (OTH) AF: 0.373 AC: 786 AN: 2110

Alfa AF: 0.413 Hom.: 41286

Bravo AF: 0.350

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.2
DANN	Benign	0.90
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7084722; hg19: chr10-16595396;