6-22746908-T-C

Position:

• chr6-22746908-T-C

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22746908T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000233358	ENST00000420572.2	n.198-1840A>G		intron_variant		3

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

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.855

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9460779; hg19: chr6-22747137;