ENST00000664438.1:n.112+42016G>T

Variant names:

• chr9-13488609-G-T
• rs4741304
• ENST00000664438.1:n.112+42016G>T

Variant summary

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

The ENST00000664438.1(ENSG00000226197):​n.112+42016G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,178 control chromosomes in the GnomAD database, including 63,732 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 0.91 (63732 hom., cov: 32)
• Consequence: ENSG00000226197 ENST00000664438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.112+42016G>T		intron	N/A
	ENSG00000226197	ENST00000664700.2		n.371+1252G>T		intron	N/A
	ENSG00000226197	ENST00000690341.3		n.173-19329G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138978 AN: 152060 Hom.: 63674 Cov.: 32

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.914 AC: 139096 AN: 152178 Hom.: 63732 Cov.: 32 AF XY: 0.917 AC XY: 68187 AN XY: 74378

African (AFR) AF: 0.977 AC: 40616 AN: 41566

American (AMR) AF: 0.920 AC: 14036 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3115 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5152 AN: 5156

South Asian (SAS) AF: 0.968 AC: 4668 AN: 4820

European-Finnish (FIN) AF: 0.893 AC: 9460 AN: 10596

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59167 AN: 67988

Other (OTH) AF: 0.902 AC: 1905 AN: 2112

Alfa AF: 0.900 Hom.: 55373

Bravo AF: 0.917

Asia WGS AF: 0.983 AC: 3418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4741304; hg19: chr9-13488608;