9-87142805-G-T

Variant names:

• chr9-87142805-G-T
• rs277729
• ENST00000836246.1:n.1352-25896C>A

Variant summary

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

The ENST00000836246.1(ENSG00000288903):​n.1352-25896C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 151,728 control chromosomes in the GnomAD database, including 55,416 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 0.85 (55416 hom., cov: 30)
• Consequence: ENSG00000288903 ENST00000836246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 2 publications found

Genes affected

ENSG00000288903 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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
ENSG00000288903	ENST00000836246.1	n.1352-25896C>A		intron_variant	Intron 7 of 8
ENSG00000288903	ENST00000836247.1	n.1302-25896C>A		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129293 AN: 151608 Hom.: 55372 Cov.: 30

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.853 AC: 129396 AN: 151728 Hom.: 55416 Cov.: 30 AF XY: 0.856 AC XY: 63469 AN XY: 74130

African (AFR) AF: 0.911 AC: 37742 AN: 41410

American (AMR) AF: 0.882 AC: 13461 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3124 AN: 3462

East Asian (EAS) AF: 0.954 AC: 4884 AN: 5122

South Asian (SAS) AF: 0.830 AC: 3983 AN: 4800

European-Finnish (FIN) AF: 0.850 AC: 8945 AN: 10518

Middle Eastern (MID) AF: 0.921 AC: 269 AN: 292

European-Non Finnish (NFE) AF: 0.800 AC: 54300 AN: 67842

Other (OTH) AF: 0.861 AC: 1814 AN: 2106

Alfa AF: 0.776 Hom.: 2222

Bravo AF: 0.862

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.95
DANN	Benign	0.56
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs277729; hg19: chr9-89757720;