9-7925381-T-G

Variant names:

• chr9-7925381-T-G
• rs1535480
• ENST00000656028.1:n.702+164A>C

Variant summary

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

The ENST00000656028.1(ENSG00000231902):​n.702+164A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,966 control chromosomes in the GnomAD database, including 13,708 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 0.42 (13708 hom., cov: 32)
• Consequence: ENSG00000231902 ENST00000656028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 8 publications found

Genes affected

ENSG00000231902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656028.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231902	ENST00000656028.1		n.702+164A>C		intron	N/A
	ENSG00000231902	ENST00000668681.2		n.571+164A>C		intron	N/A
	ENSG00000231902	ENST00000813700.1		n.568+164A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63184 AN: 151848 Hom.: 13702 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.416 AC: 63229 AN: 151966 Hom.: 13708 Cov.: 32 AF XY: 0.419 AC XY: 31110 AN XY: 74252

African (AFR) AF: 0.388 AC: 16064 AN: 41454

American (AMR) AF: 0.519 AC: 7913 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1415 AN: 3470

East Asian (EAS) AF: 0.706 AC: 3628 AN: 5136

South Asian (SAS) AF: 0.515 AC: 2481 AN: 4816

European-Finnish (FIN) AF: 0.353 AC: 3725 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26814 AN: 67962

Other (OTH) AF: 0.412 AC: 868 AN: 2106

Alfa AF: 0.409 Hom.: 39424

Bravo AF: 0.429

Asia WGS AF: 0.542 AC: 1881 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1535480; hg19: chr9-7925381;