rs9659297

Variant names:

• chr1-238308776-A-G
• rs9659297
• ENST00000665394.1:n.194-16989A>G

Variant summary

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

The ENST00000665394.1(ENSG00000234464):​n.194-16989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,146 control chromosomes in the GnomAD database, including 3,962 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 0.21 (3962 hom., cov: 32)
• Consequence: ENSG00000234464 ENST00000665394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 1 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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
ENSG00000234464	ENST00000665394.1	n.194-16989A>G		intron_variant	Intron 2 of 4
ENSG00000234464	ENST00000716147.1	n.369-16989A>G		intron_variant	Intron 3 of 6
ENSG00000234464	ENST00000716149.1	n.328-16989A>G		intron_variant	Intron 3 of 6
ENSG00000234464	ENST00000716150.1	n.186-16989A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31229 AN: 152030 Hom.: 3950 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.206 AC: 31276 AN: 152146 Hom.: 3962 Cov.: 32 AF XY: 0.205 AC XY: 15254 AN XY: 74388

African (AFR) AF: 0.364 AC: 15088 AN: 41484

American (AMR) AF: 0.208 AC: 3170 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3470

East Asian (EAS) AF: 0.118 AC: 610 AN: 5174

South Asian (SAS) AF: 0.234 AC: 1131 AN: 4826

European-Finnish (FIN) AF: 0.149 AC: 1585 AN: 10608

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8456 AN: 68000

Other (OTH) AF: 0.213 AC: 450 AN: 2110

Alfa AF: 0.154 Hom.: 1210

Bravo AF: 0.221

Asia WGS AF: 0.228 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.28
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs9659297; hg19: chr1-238472076;