chr9-102254467-G-A

Variant names:

• chr9-102254467-G-A
• rs1535628
• ENST00000737266.1:n.138-4718G>A

Variant summary

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

The ENST00000737266.1(ENSG00000296202):​n.138-4718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,048 control chromosomes in the GnomAD database, including 3,348 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 0.16 (3348 hom., cov: 32)
• Consequence: ENSG00000296202 ENST00000737266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 5 publications found

Genes affected

ENSG00000296202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376188	XR_930189.2	n.190-4718G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296202	ENST00000737266.1	n.138-4718G>A		intron_variant	Intron 2 of 2
ENSG00000296202	ENST00000737267.1	n.523-4718G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24794 AN: 151930 Hom.: 3351 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.163 AC: 24822 AN: 152048 Hom.: 3348 Cov.: 32 AF XY: 0.170 AC XY: 12608 AN XY: 74332

African (AFR) AF: 0.245 AC: 10146 AN: 41480

American (AMR) AF: 0.153 AC: 2328 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3659 AN: 5130

South Asian (SAS) AF: 0.351 AC: 1694 AN: 4822

European-Finnish (FIN) AF: 0.0443 AC: 469 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0852 AC: 5788 AN: 67972

Other (OTH) AF: 0.160 AC: 337 AN: 2110

Alfa AF: 0.116 Hom.: 853

Bravo AF: 0.175

Asia WGS AF: 0.474 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.40
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1535628; hg19: chr9-105016749;