rs9891455

Variant names:

• chr17-32132039-T-C
• rs9891455
• ENST00000830768.1:n.276+4170T>C

Variant summary

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

The ENST00000830768.1(ENSG00000277511):​n.276+4170T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,118 control chromosomes in the GnomAD database, including 6,994 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 0.27 (6994 hom., cov: 32)
• Consequence: ENSG00000277511 ENST00000830768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 4 publications found

Genes affected

ENSG00000277511 (HGNC:56888):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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
ENSG00000277511	ENST00000830768.1	n.276+4170T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40524 AN: 152000 Hom.: 6962 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.267 AC: 40608 AN: 152118 Hom.: 6994 Cov.: 32 AF XY: 0.264 AC XY: 19614 AN XY: 74384

African (AFR) AF: 0.492 AC: 20406 AN: 41456

American (AMR) AF: 0.215 AC: 3284 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1145 AN: 5182

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4820

European-Finnish (FIN) AF: 0.137 AC: 1451 AN: 10600

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11629 AN: 67992

Other (OTH) AF: 0.240 AC: 508 AN: 2114

Alfa AF: 0.237 Hom.: 915

Bravo AF: 0.281

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.81
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs9891455; hg19: chr17-30459058;