rs12000445

Positions:

• chr9-23426273-A-G

Variant summary

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

The ENST00000640003.1(ENSG00000284418):​n.139+12289T>C 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 0.177 in 152,120 control chromosomes in the GnomAD database, including 3,890 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 0.18 (3890 hom., cov: 32)
• Consequence: ENST00000640003.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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 = 0.389 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
	ENST00000640003.1	n.139+12289T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000664493.1	n.110+12289T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26879 AN: 152002 Hom.: 3890 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.177 AC: 26904 AN: 152120 Hom.: 3890 Cov.: 32 AF XY: 0.175 AC XY: 13013 AN XY: 74390

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0687

Gnomad4 OTH AF: 0.173

Alfa AF: 0.107 Hom.: 802

Bravo AF: 0.197

Asia WGS AF: 0.212 AC: 740 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	0.62
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12000445; hg19: chr9-23426271;