22-28831983-G-A

Variant names:

• chr22-28831983-G-A
• rs6005907
• ENST00000418292.1:n.35-6877G>A

Variant summary

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

The ENST00000418292.1(ENSG00000226471):​n.35-6877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,074 control chromosomes in the GnomAD database, including 1,513 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 0.12 (1513 hom., cov: 31)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 11 publications found

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418292.1. 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
	ENSG00000226471	ENST00000418292.1	TSL:3	n.35-6877G>A		intron	N/A
	ENSG00000226471	ENST00000458080.2	TSL:3	n.263+9804G>A		intron	N/A
	ENSG00000226471	ENST00000687270.2		n.268+9804G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17471 AN: 151956 Hom.: 1508 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.115 AC: 17518 AN: 152074 Hom.: 1513 Cov.: 31 AF XY: 0.114 AC XY: 8507 AN XY: 74338

African (AFR) AF: 0.227 AC: 9412 AN: 41460

American (AMR) AF: 0.103 AC: 1577 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0704 AC: 244 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1429 AN: 5160

South Asian (SAS) AF: 0.0650 AC: 313 AN: 4818

European-Finnish (FIN) AF: 0.0633 AC: 670 AN: 10588

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3593 AN: 67994

Other (OTH) AF: 0.0999 AC: 211 AN: 2112

Alfa AF: 0.0742 Hom.: 2866

Bravo AF: 0.125

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6005907; hg19: chr22-29227971;