rs11625623

Variant names:

• chr14-52292628-A-G
• rs11625623
• ENST00000726797.1:n.299+20208T>C

Variant summary

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

The ENST00000726797.1(ENSG00000289424):​n.299+20208T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,976 control chromosomes in the GnomAD database, including 3,245 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 0.20 (3245 hom., cov: 32)
• Consequence: ENSG00000289424 ENST00000726797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 1 publications found

Genes affected

ENSG00000289424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 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
ENSG00000289424	ENST00000726797.1	n.299+20208T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30810 AN: 151858 Hom.: 3235 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.203 AC: 30841 AN: 151976 Hom.: 3245 Cov.: 32 AF XY: 0.203 AC XY: 15121 AN XY: 74322

African (AFR) AF: 0.176 AC: 7297 AN: 41498

American (AMR) AF: 0.164 AC: 2500 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3470

East Asian (EAS) AF: 0.138 AC: 714 AN: 5184

South Asian (SAS) AF: 0.343 AC: 1653 AN: 4818

European-Finnish (FIN) AF: 0.168 AC: 1761 AN: 10478

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.223 AC: 15163 AN: 67936

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.214 Hom.: 467

Bravo AF: 0.198

Asia WGS AF: 0.213 AC: 730 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs11625623; hg19: chr14-52759346;