rs1904173

Positions:

• chr5-25419980-G-A

Variant summary

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

The ENST00000507887.5(ENSG00000248605):​n.232+2750C>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 0.169 in 152,002 control chromosomes in the GnomAD database, including 2,442 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 0.17 (2442 hom., cov: 32)
• Consequence: ENST00000507887.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507887.5	n.232+2750C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000507926.1	n.214+2750C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000511029.5	n.126+2750C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25599 AN: 151884 Hom.: 2431 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.169 AC: 25625 AN: 152002 Hom.: 2442 Cov.: 32 AF XY: 0.168 AC XY: 12499 AN XY: 74280

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.125

Alfa AF: 0.142 Hom.: 2856

Bravo AF: 0.161

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1904173; hg19: chr5-25420089;