chr9-27768411-T-G

Variant names:

• chr9-27768411-T-G
• rs1774026
• ENST00000727209.1:n.116-15785A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000727209.1(ENSG00000294991):​n.116-15785A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,100 control chromosomes in the GnomAD database, including 63,193 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 0.90 (63193 hom., cov: 33)
• Consequence: ENSG00000294991 ENST00000727209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961
• Publications: 2 publications found

Genes affected

ENSG00000294991 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 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
ENSG00000294991	ENST00000727209.1	n.116-15785A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137256 AN: 151982 Hom.: 63181 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.903 AC: 137312 AN: 152100 Hom.: 63193 Cov.: 33 AF XY: 0.904 AC XY: 67203 AN XY: 74346

African (AFR) AF: 0.704 AC: 29197 AN: 41464

American (AMR) AF: 0.938 AC: 14316 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3442 AN: 3468

East Asian (EAS) AF: 0.926 AC: 4776 AN: 5158

South Asian (SAS) AF: 0.896 AC: 4316 AN: 4816

European-Finnish (FIN) AF: 0.997 AC: 10595 AN: 10624

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67535 AN: 67982

Other (OTH) AF: 0.920 AC: 1945 AN: 2114

Alfa AF: 0.954 Hom.: 11112

Bravo AF: 0.892

Asia WGS AF: 0.863 AC: 3001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	17
DANN	Benign	0.86
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs1774026; hg19: chr9-27768409;