ENST00000664438.1:n.163-81120T>C

Variant names:

• chr9-13755193-T-C
• rs1011531
• ENST00000664438.1:n.163-81120T>C

Variant summary

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

The ENST00000664438.1(ENSG00000226197):​n.163-81120T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,942 control chromosomes in the GnomAD database, including 24,475 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 0.55 (24475 hom., cov: 31)
• Consequence: ENSG00000226197 ENST00000664438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 5 publications found

Genes affected

ENSG00000226197 (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 = 0.873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664438.1. 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
	ENSG00000226197	ENST00000664438.1		n.163-81120T>C		intron	N/A
	ENSG00000289185	ENST00000741129.1		n.1194-42504A>G		intron	N/A
	ENSG00000289185	ENST00000741130.1		n.1688-15573A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83765 AN: 151824 Hom.: 24457 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.552 AC: 83810 AN: 151942 Hom.: 24475 Cov.: 31 AF XY: 0.559 AC XY: 41497 AN XY: 74262

African (AFR) AF: 0.371 AC: 15345 AN: 41414

American (AMR) AF: 0.607 AC: 9257 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2108 AN: 3470

East Asian (EAS) AF: 0.894 AC: 4610 AN: 5156

South Asian (SAS) AF: 0.746 AC: 3598 AN: 4822

European-Finnish (FIN) AF: 0.653 AC: 6896 AN: 10562

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40087 AN: 67948

Other (OTH) AF: 0.556 AC: 1175 AN: 2112

Alfa AF: 0.591 Hom.: 15727

Bravo AF: 0.541

Asia WGS AF: 0.778 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1011531; hg19: chr9-13755192;