rs2227744

chr5-76714524-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507514.1(ENSG00000225407):n.39+1653C>T variant causes a intron, non coding transcript 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: ENST00000507514.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000507514.1	n.39+1653C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.401

Alfa AF: 0.435 Hom.: 19845

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227744; hg19: chr5-76010349;