rs2227744

Variant names:

• chr5-76714524-G-A
• rs2227744
• ENST00000507514.1:n.39+1653C>T

Variant summary

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

The ENST00000507514.1(ENSG00000225407):​n.39+1653C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,056 control chromosomes in the GnomAD database, including 11,549 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 0.38 (11549 hom., cov: 33)
• Consequence: ENSG00000225407 ENST00000507514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 15 publications found

Genes affected

ENSG00000225407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 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
ENSG00000225407	ENST00000507514.1	n.39+1653C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57041 AN: 151936 Hom.: 11549 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.375 AC: 57035 AN: 152056 Hom.: 11549 Cov.: 33 AF XY: 0.372 AC XY: 27644 AN XY: 74304

African (AFR) AF: 0.242 AC: 10059 AN: 41486

American (AMR) AF: 0.365 AC: 5579 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1289 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1544 AN: 5170

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4814

European-Finnish (FIN) AF: 0.475 AC: 5017 AN: 10554

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31119 AN: 67970

Other (OTH) AF: 0.401 AC: 847 AN: 2112

Alfa AF: 0.427 Hom.: 24374

Bravo AF: 0.364

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.79
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2227744; hg19: chr5-76010349;