rs7287806

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000226471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226471	ENST00000418292.1	n.34+16286G>A		intron_variant	Intron 1 of 1	3
ENSG00000226471	ENST00000451486.5	n.104-4949G>A		intron_variant	Intron 1 of 1	5
ENSG00000226471	ENST00000458080.1	n.56-4949G>A		intron_variant	Intron 1 of 3	3

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

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.400

Alfa AF: 0.345 Hom.: 5377

Bravo AF: 0.432

Asia WGS AF: 0.618 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7287806; hg19: chr22-29213011;