rs10818721

chr9-122586802-T-G

Variant summary

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

The ENST00000431442.2(ENSG00000234156):n.1363-19844T>G 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 0.277 in 152,074 control chromosomes in the GnomAD database, including 6,460 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 0.28 (6460 hom., cov: 31)
• Consequence: ENST00000431442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.579 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
	ENST00000431442.2	n.1363-19844T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42048 AN: 151954 Hom.: 6449 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.277 AC: 42095 AN: 152074 Hom.: 6460 Cov.: 31 AF XY: 0.284 AC XY: 21087 AN XY: 74346

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.296

Alfa AF: 0.262 Hom.: 6234

Bravo AF: 0.289

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.9
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10818721; hg19: chr9-125349081;