chr9-13557492-A-C

Variant names:

• chr9-13557492-A-C
• rs1324183
• ENST00000664438.1:n.162+4168A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664438.1(ENSG00000226197):​n.162+4168A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,014 control chromosomes in the GnomAD database, including 45,876 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 0.77 (45876 hom., cov: 32)
• Consequence: ENSG00000226197 ENST00000664438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ENSG00000226197 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226197	ENST00000664438.1	n.162+4168A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117669 AN: 151896 Hom.: 45849 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.775 AC: 117747 AN: 152014 Hom.: 45876 Cov.: 32 AF XY: 0.777 AC XY: 57733 AN XY: 74296

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.761

Alfa AF: 0.782 Hom.: 17897

Bravo AF: 0.773

Asia WGS AF: 0.754 AC: 2620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324183; hg19: chr9-13557491;