rs7725052

Positions:

• chr5-40487168-C-T

Variant summary

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

The ENST00000648975.1(ENSG00000285616):​n.2420+843G>A 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 0.515 in 151,932 control chromosomes in the GnomAD database, including 20,936 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 (20936 hom., cov: 32)
• Consequence: ENST00000648975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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
	ENST00000648975.1	n.2420+843G>A		intron_variant, non_coding_transcript_variant
	ENST00000649444.1	n.242+670C>T		intron_variant, non_coding_transcript_variant
	ENST00000649894.1	n.120-16703C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78219 AN: 151814 Hom.: 20918 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.515 AC: 78270 AN: 151932 Hom.: 20936 Cov.: 32 AF XY: 0.504 AC XY: 37435 AN XY: 74264

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.503

Alfa AF: 0.549 Hom.: 2878

Bravo AF: 0.518

Asia WGS AF: 0.237 AC: 825 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7725052; hg19: chr5-40487270;