rs888229

chr9-126156171-G-Achr9-126156171-G-T

Variant summary

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

The ENST00000441473.1(ENSG00000232413):n.236-3362G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,062 control chromosomes in the GnomAD database, including 4,767 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 0.24 (4767 hom., cov: 32)
• Consequence: ENST00000441473.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000441473.1	n.236-3362G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36989 AN: 151944 Hom.: 4756 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.244 AC: 37032 AN: 152062 Hom.: 4767 Cov.: 32 AF XY: 0.242 AC XY: 17998 AN XY: 74330

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.249

Alfa AF: 0.200 Hom.: 1527

Bravo AF: 0.255

Asia WGS AF: 0.265 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.091
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs888229; hg19: chr9-128918450;