rs738806

Variant names:

• chr22-23891985-A-G
• rs738806
• ENST00000433835.3:c.432-2787A>G

Variant summary

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

The ENST00000433835.3(ENSG00000251357):​c.432-2787A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,182 control chromosomes in the GnomAD database, including 44,288 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 0.76 (44288 hom., cov: 32)
• Consequence: ENSG00000251357 ENST00000433835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 32 publications found

Genes affected

ENSG00000251357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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
ENSG00000251357	ENST00000433835.3	c.432-2787A>G		intron_variant	Intron 4 of 5	5		ENSP00000400325.3
ENSG00000290199	ENST00000717616.1	n.213-519T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115918 AN: 152064 Hom.: 44249 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.762 AC: 116011 AN: 152182 Hom.: 44288 Cov.: 32 AF XY: 0.764 AC XY: 56852 AN XY: 74398

African (AFR) AF: 0.801 AC: 33280 AN: 41528

American (AMR) AF: 0.784 AC: 11995 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2456 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3380 AN: 5168

South Asian (SAS) AF: 0.738 AC: 3557 AN: 4822

European-Finnish (FIN) AF: 0.785 AC: 8311 AN: 10592

Middle Eastern (MID) AF: 0.846 AC: 247 AN: 292

European-Non Finnish (NFE) AF: 0.741 AC: 50387 AN: 67982

Other (OTH) AF: 0.750 AC: 1585 AN: 2114

Alfa AF: 0.748 Hom.: 192309

Bravo AF: 0.764

Asia WGS AF: 0.714 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs738806; hg19: chr22-24234172;