rs10757878

Variant names:

• chr9-29504222-A-G
• rs10757878
• ENST00000850880.1:n.99-48545A>G

Variant summary

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

The ENST00000850880.1(ENSG00000300941):​n.99-48545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,120 control chromosomes in the GnomAD database, including 32,993 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 0.66 (32993 hom., cov: 33)
• Consequence: ENSG00000300941 ENST00000850880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 1 publications found

Genes affected

ENSG00000300941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 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
ENSG00000300941	ENST00000850880.1	n.99-48545A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99619 AN: 152002 Hom.: 32955 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.656 AC: 99716 AN: 152120 Hom.: 32993 Cov.: 33 AF XY: 0.657 AC XY: 48849 AN XY: 74370

African (AFR) AF: 0.688 AC: 28536 AN: 41506

American (AMR) AF: 0.712 AC: 10896 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4331 AN: 5158

South Asian (SAS) AF: 0.530 AC: 2552 AN: 4814

European-Finnish (FIN) AF: 0.659 AC: 6970 AN: 10576

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42583 AN: 67976

Other (OTH) AF: 0.640 AC: 1355 AN: 2116

Alfa AF: 0.639 Hom.: 6303

Bravo AF: 0.664

Asia WGS AF: 0.692 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.93
DANN	Benign	0.62
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10757878; hg19: chr9-29504220;