chr9-101004255-G-A

Variant names:

• chr9-101004255-G-A
• rs2417226
• ENST00000727919.1:n.93-9205C>T

Variant summary

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

The ENST00000727919.1(ENSG00000295090):​n.93-9205C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,566 control chromosomes in the GnomAD database, including 2,855 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 0.18 (2855 hom., cov: 30)
• Consequence: ENSG00000295090 ENST00000727919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

Genes affected

ENSG00000295090 (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 (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727919.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295090	ENST00000727919.1		n.93-9205C>T		intron	N/A
	ENSG00000295090	ENST00000727920.1		n.92-9207C>T		intron	N/A
	ENSG00000295090	ENST00000727921.1		n.93-10927C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26683 AN: 151448 Hom.: 2848 Cov.: 30

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.176 AC: 26710 AN: 151566 Hom.: 2855 Cov.: 30 AF XY: 0.184 AC XY: 13604 AN XY: 73990

African (AFR) AF: 0.155 AC: 6396 AN: 41314

American (AMR) AF: 0.159 AC: 2413 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3466

East Asian (EAS) AF: 0.480 AC: 2453 AN: 5112

South Asian (SAS) AF: 0.415 AC: 1978 AN: 4766

European-Finnish (FIN) AF: 0.191 AC: 2003 AN: 10504

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10487 AN: 67910

Other (OTH) AF: 0.183 AC: 384 AN: 2098

Alfa AF: 0.156 Hom.: 509

Bravo AF: 0.169

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.69
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2417226; hg19: chr9-103766537;