chr9-27769783-C-G

Variant names:

• chr9-27769783-C-G
• rs1330197
• ENST00000727209.1:n.116-17157G>C

Variant summary

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

The ENST00000727209.1(ENSG00000294991):​n.116-17157G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,106 control chromosomes in the GnomAD database, including 66,249 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 0.93 (66249 hom., cov: 32)
• Consequence: ENSG00000294991 ENST00000727209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 2 publications found

Genes affected

ENSG00000294991 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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.116-17157G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141284 AN: 151988 Hom.: 66226 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.929 AC: 141361 AN: 152106 Hom.: 66249 Cov.: 32 AF XY: 0.929 AC XY: 69097 AN XY: 74368

African (AFR) AF: 0.800 AC: 33177 AN: 41460

American (AMR) AF: 0.936 AC: 14281 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3446 AN: 3472

East Asian (EAS) AF: 0.927 AC: 4797 AN: 5176

South Asian (SAS) AF: 0.896 AC: 4313 AN: 4812

European-Finnish (FIN) AF: 0.997 AC: 10596 AN: 10624

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67576 AN: 67988

Other (OTH) AF: 0.940 AC: 1984 AN: 2110

Alfa AF: 0.973 Hom.: 3458

Bravo AF: 0.924

Asia WGS AF: 0.870 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.66
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1330197; hg19: chr9-27769781;