rs306776

Variant names:

• chr9-121431890-C-A
• rs306776
• ENST00000440807.1:n.86-8486C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-121431890-C-A
• chr9-121431890-C-G

Variant summary

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

The ENST00000440807.1(ENSG00000227355):​n.86-8486C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 152,128 control chromosomes in the GnomAD database, including 64,529 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 0.92 (64529 hom., cov: 30)
• Consequence: ENSG00000227355 ENST00000440807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 0 publications found

Genes affected

ENSG00000227355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723324	NR_187153.1	n.405-30767C>A		intron_variant	Intron 2 of 3
LOC102723324	NR_187154.1	n.208-30767C>A		intron_variant	Intron 2 of 3
LOC102723324	NR_187158.1	n.170-30767C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227355	ENST00000440807.1	n.86-8486C>A		intron_variant	Intron 1 of 2	3
ENSG00000227355	ENST00000635872.1	n.157-30767C>A		intron_variant	Intron 2 of 3	3
ENSG00000227355	ENST00000658975.2	n.170-8486C>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139435 AN: 152010 Hom.: 64500 Cov.: 30

Gnomad AFR AF: 0.838

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.917 AC: 139519 AN: 152128 Hom.: 64529 Cov.: 30 AF XY: 0.913 AC XY: 67916 AN XY: 74354

African (AFR) AF: 0.838 AC: 34731 AN: 41466

American (AMR) AF: 0.827 AC: 12616 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 3370 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3779 AN: 5162

South Asian (SAS) AF: 0.917 AC: 4414 AN: 4814

European-Finnish (FIN) AF: 0.971 AC: 10313 AN: 10616

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67141 AN: 68016

Other (OTH) AF: 0.926 AC: 1957 AN: 2114

Alfa AF: 0.941 Hom.: 9413

Bravo AF: 0.902

Asia WGS AF: 0.837 AC: 2911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs306776; hg19: chr9-124194168;