rs268147

chr5-126224886-T-C

Variant summary

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

The ENST00000651847.1(ENSG00000248752):n.77-29657A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.899 in 152,240 control chromosomes in the GnomAD database, including 61,850 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 0.90 (61850 hom., cov: 32)
• Consequence: ENST00000651847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901056	XR_007058919.1	n.1620-126725A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651847.1	n.77-29657A>G		intron_variant, non_coding_transcript_variant
	ENST00000450613.2	n.71+54845A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136815 AN: 152122 Hom.: 61788 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.899 AC: 136936 AN: 152240 Hom.: 61850 Cov.: 32 AF XY: 0.901 AC XY: 67033 AN XY: 74418

Gnomad4 AFR AF: 0.974

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.891

Alfa AF: 0.877 Hom.: 7303

Bravo AF: 0.903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.0
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs268147; hg19: chr5-125560579;