chr9-104530034-T-C

Variant names:

• chr9-104530034-T-C
• rs1523670
• ENST00000635678.1:n.348-5892T>C

Variant summary

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

The ENST00000635678.1(ENSG00000283001):​n.348-5892T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,016 control chromosomes in the GnomAD database, including 12,028 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 0.39 (12028 hom., cov: 32)
• Consequence: ENSG00000283001 ENST00000635678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 0 publications found

Genes affected

ENSG00000283001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635678.1. 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
	ENSG00000283001	ENST00000635678.1	TSL:5	n.348-5892T>C		intron	N/A
	ENSG00000283001	ENST00000653242.1		n.299-5892T>C		intron	N/A
	ENSG00000283001	ENST00000658313.1		n.101-5892T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59186 AN: 151896 Hom.: 12013 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.390 AC: 59249 AN: 152016 Hom.: 12028 Cov.: 32 AF XY: 0.396 AC XY: 29459 AN XY: 74306

African (AFR) AF: 0.447 AC: 18553 AN: 41494

American (AMR) AF: 0.339 AC: 5163 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1118 AN: 3466

East Asian (EAS) AF: 0.724 AC: 3736 AN: 5158

South Asian (SAS) AF: 0.541 AC: 2603 AN: 4812

European-Finnish (FIN) AF: 0.395 AC: 4181 AN: 10578

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

European-Non Finnish (NFE) AF: 0.333 AC: 22650 AN: 67946

Other (OTH) AF: 0.389 AC: 821 AN: 2108

Alfa AF: 0.355 Hom.: 5218

Bravo AF: 0.387

Asia WGS AF: 0.619 AC: 2149 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.30
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1523670; hg19: chr9-107292315;