rs1022455

Variant names:

• chr16-25518069-T-A
• rs1022455
• ENST00000736532.1:n.204+22063T>A

Variant summary

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

The ENST00000736532.1(ENSG00000296116):​n.204+22063T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,018 control chromosomes in the GnomAD database, including 22,467 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 0.52 (22467 hom., cov: 32)
• Consequence: ENSG00000296116 ENST00000736532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

ENSG00000296116 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 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
ENSG00000296116	ENST00000736532.1	n.204+22063T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79186 AN: 151900 Hom.: 22443 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.521 AC: 79259 AN: 152018 Hom.: 22467 Cov.: 32 AF XY: 0.513 AC XY: 38152 AN XY: 74312

African (AFR) AF: 0.746 AC: 30924 AN: 41476

American (AMR) AF: 0.409 AC: 6238 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1037 AN: 5158

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4814

European-Finnish (FIN) AF: 0.439 AC: 4640 AN: 10572

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31336 AN: 67958

Other (OTH) AF: 0.476 AC: 1005 AN: 2110

Alfa AF: 0.498 Hom.: 2464

Bravo AF: 0.528

Asia WGS AF: 0.362 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1022455; hg19: chr16-25529390;