chr6-22746908-T-C

Variant names:

• chr6-22746908-T-C
• rs9460779
• ENST00000420572.2:n.198-1840A>G

Variant summary

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

The ENST00000420572.2(ENSG00000233358):​n.198-1840A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 151,876 control chromosomes in the GnomAD database, including 52,887 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 0.83 (52887 hom., cov: 32)
• Consequence: ENSG00000233358 ENST00000420572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 2 publications found

Genes affected

ENSG00000233358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420572.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233358	ENST00000420572.2	TSL:3	n.198-1840A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126523 AN: 151758 Hom.: 52865 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.834 AC: 126596 AN: 151876 Hom.: 52887 Cov.: 32 AF XY: 0.831 AC XY: 61673 AN XY: 74212

African (AFR) AF: 0.813 AC: 33685 AN: 41444

American (AMR) AF: 0.814 AC: 12403 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3152 AN: 3466

East Asian (EAS) AF: 0.732 AC: 3748 AN: 5122

South Asian (SAS) AF: 0.724 AC: 3482 AN: 4812

European-Finnish (FIN) AF: 0.857 AC: 9071 AN: 10586

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58174 AN: 67894

Other (OTH) AF: 0.855 AC: 1805 AN: 2112

Alfa AF: 0.817 Hom.: 4993

Bravo AF: 0.834

Asia WGS AF: 0.749 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs9460779; hg19: chr6-22747137;