rs7287806

Variant names:

• chr22-28817023-G-A
• rs7287806
• ENST00000418292.1:n.34+16286G>A

Variant summary

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

The ENST00000418292.1(ENSG00000226471):​n.34+16286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,886 control chromosomes in the GnomAD database, including 16,024 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 0.43 (16024 hom., cov: 31)
• Consequence: ENSG00000226471 ENST00000418292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 12 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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

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
	ENSG00000226471	ENST00000418292.1	TSL:3	n.34+16286G>A		intron	N/A
	ENSG00000226471	ENST00000451486.5	TSL:5	n.104-4949G>A		intron	N/A
	ENSG00000226471	ENST00000458080.2	TSL:3	n.56-4949G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64979 AN: 151768 Hom.: 15975 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.429 AC: 65091 AN: 151886 Hom.: 16024 Cov.: 31 AF XY: 0.430 AC XY: 31909 AN XY: 74230

African (AFR) AF: 0.659 AC: 27281 AN: 41414

American (AMR) AF: 0.311 AC: 4739 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3478 AN: 5152

South Asian (SAS) AF: 0.536 AC: 2581 AN: 4814

European-Finnish (FIN) AF: 0.364 AC: 3843 AN: 10568

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20901 AN: 67912

Other (OTH) AF: 0.400 AC: 843 AN: 2108

Alfa AF: 0.347 Hom.: 5986

Bravo AF: 0.432

Asia WGS AF: 0.618 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7287806; hg19: chr22-29213011;