rs6007127

Variant names:

• chr22-45646655-G-A
• rs6007127
• ENST00000829473.1:n.162+547G>A

Variant summary

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

The ENST00000829473.1(ENSG00000307862):​n.162+547G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,182 control chromosomes in the GnomAD database, including 1,275 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 0.097 (1275 hom., cov: 32)
• Consequence: ENSG00000307862 ENST00000829473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 1 publications found

Genes affected

ENSG00000307862 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829473.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307862	ENST00000829473.1		n.162+547G>A		intron	N/A
	ENSG00000307862	ENST00000829474.1		n.810+19G>A		intron	N/A
	ENSG00000307862	ENST00000829475.1		n.266-104G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14715 AN: 152064 Hom.: 1270 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0606

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0776

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

GnomAD4 genome AF: 0.0969 AC: 14748 AN: 152182 Hom.: 1275 Cov.: 32 AF XY: 0.0958 AC XY: 7125 AN XY: 74394

African (AFR) AF: 0.237 AC: 9838 AN: 41490

American (AMR) AF: 0.0605 AC: 925 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4820

European-Finnish (FIN) AF: 0.0651 AC: 690 AN: 10592

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0409 AC: 2782 AN: 68012

Other (OTH) AF: 0.0773 AC: 163 AN: 2110

Alfa AF: 0.0830 Hom.: 150

Bravo AF: 0.103

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.28
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs6007127; hg19: chr22-46042535;