6-125410784-T-C

Variant names:

• chr6-125410784-T-C
• rs9321038
• ENST00000422227.2:n.160+34238A>G

Variant summary

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

The ENST00000422227.2(ENSG00000226409):​n.160+34238A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,234 control chromosomes in the GnomAD database, including 48,017 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 0.78 (48017 hom., cov: 34)
• Consequence: ENSG00000226409 ENST00000422227.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 3 publications found

Genes affected

ENSG00000226409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723341	NR_187738.1	n.159-2162A>G		intron_variant	Intron 1 of 4
LOC102723341	NR_187739.1	n.295+27296A>G		intron_variant	Intron 2 of 4
LOC102723341	NR_187740.1	n.158+34238A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226409	ENST00000422227.2	n.160+34238A>G		intron_variant	Intron 1 of 3	5
ENSG00000226409	ENST00000638742.2	n.153-2162A>G		intron_variant	Intron 1 of 4	5
ENSG00000226409	ENST00000640550.1	n.267+27296A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118527 AN: 152116 Hom.: 47990 Cov.: 34

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.779 AC: 118603 AN: 152234 Hom.: 48017 Cov.: 34 AF XY: 0.783 AC XY: 58272 AN XY: 74422

African (AFR) AF: 0.533 AC: 22132 AN: 41506

American (AMR) AF: 0.857 AC: 13107 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2668 AN: 3468

East Asian (EAS) AF: 0.922 AC: 4782 AN: 5186

South Asian (SAS) AF: 0.776 AC: 3747 AN: 4826

European-Finnish (FIN) AF: 0.938 AC: 9954 AN: 10612

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59560 AN: 68020

Other (OTH) AF: 0.800 AC: 1692 AN: 2116

Alfa AF: 0.842 Hom.: 88740

Bravo AF: 0.763

Asia WGS AF: 0.816 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs9321038; hg19: chr6-125731930;