9-80269662-C-T

Variant names:

• chr9-80269662-C-T
• rs2695
• ENST00000731547.1:n.270+233C>T

Variant summary

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

The ENST00000731547.1(ENSG00000295651):​n.270+233C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,992 control chromosomes in the GnomAD database, including 7,350 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 0.30 (7350 hom., cov: 32)
• Consequence: ENSG00000295651 ENST00000731547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 20 publications found

Genes affected

ENSG00000295651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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
ENSG00000295651	ENST00000731547.1	n.270+233C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45456 AN: 151874 Hom.: 7336 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.299 AC: 45495 AN: 151992 Hom.: 7350 Cov.: 32 AF XY: 0.305 AC XY: 22679 AN XY: 74280

African (AFR) AF: 0.255 AC: 10553 AN: 41446

American (AMR) AF: 0.453 AC: 6924 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2421 AN: 5150

South Asian (SAS) AF: 0.359 AC: 1733 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3290 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18660 AN: 67968

Other (OTH) AF: 0.313 AC: 660 AN: 2106

Alfa AF: 0.284 Hom.: 21202

Bravo AF: 0.308

Asia WGS AF: 0.448 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.83
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs2695; hg19: chr9-82884577;