chr10-87578876-A-C

Variant names:

• chr10-87578876-A-C
• rs9664222
• ENST00000804457.1:n.102+15926A>C

Variant summary

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

The ENST00000804457.1(ENSG00000225913):​n.102+15926A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,052 control chromosomes in the GnomAD database, including 53,842 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 0.84 (53842 hom., cov: 30)
• Consequence: ENSG00000225913 ENST00000804457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 19 publications found

Genes affected

ENSG00000225913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 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
ENSG00000225913	ENST00000804457.1	n.102+15926A>C		intron_variant	Intron 1 of 4
ENSG00000223761	ENST00000804693.1	n.211+12731T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127345 AN: 151934 Hom.: 53776 Cov.: 30

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.838 AC: 127467 AN: 152052 Hom.: 53842 Cov.: 30 AF XY: 0.838 AC XY: 62250 AN XY: 74298

African (AFR) AF: 0.942 AC: 39126 AN: 41524

American (AMR) AF: 0.845 AC: 12881 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3146 AN: 3468

East Asian (EAS) AF: 0.764 AC: 3931 AN: 5148

South Asian (SAS) AF: 0.871 AC: 4182 AN: 4804

European-Finnish (FIN) AF: 0.792 AC: 8373 AN: 10576

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53061 AN: 67970

Other (OTH) AF: 0.837 AC: 1767 AN: 2112

Alfa AF: 0.805 Hom.: 156493

Bravo AF: 0.845

Asia WGS AF: 0.833 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.7
DANN	Benign	0.41
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9664222; hg19: chr10-89338633;