chr9-122407651-C-T

Variant names:

• chr9-122407651-C-T
• rs10818684
• ENST00000431442.3:n.136+871C>T

Variant summary

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

The ENST00000431442.3(ENSG00000234156):​n.136+871C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,054 control chromosomes in the GnomAD database, including 31,448 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 0.63 (31448 hom., cov: 32)
• Consequence: ENSG00000234156 ENST00000431442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 8 publications found

Genes affected

ENSG00000234156 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 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
ENSG00000234156	ENST00000431442.3	n.136+871C>T		intron_variant	Intron 1 of 9	3
ENSG00000234156	ENST00000433572.3	n.170+2860C>T		intron_variant	Intron 2 of 6	3
ENSG00000234156	ENST00000723589.1	n.232+871C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95258 AN: 151936 Hom.: 31443 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.627 AC: 95304 AN: 152054 Hom.: 31448 Cov.: 32 AF XY: 0.625 AC XY: 46440 AN XY: 74310

African (AFR) AF: 0.407 AC: 16851 AN: 41452

American (AMR) AF: 0.619 AC: 9455 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2423 AN: 3468

East Asian (EAS) AF: 0.636 AC: 3291 AN: 5174

South Asian (SAS) AF: 0.587 AC: 2829 AN: 4822

European-Finnish (FIN) AF: 0.719 AC: 7591 AN: 10556

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50814 AN: 67990

Other (OTH) AF: 0.643 AC: 1356 AN: 2110

Alfa AF: 0.705 Hom.: 161723

Bravo AF: 0.612

Asia WGS AF: 0.551 AC: 1918 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	5.2
DANN	Benign	0.77
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10818684; hg19: chr9-125169930;