rs268147

Variant names:

• chr5-126224886-T-C
• rs268147
• ENST00000450613.2:n.71+54845A>G

Variant summary

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

The ENST00000450613.2(ENSG00000248752):​n.71+54845A>G variant causes a intron 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: ENSG00000248752 ENST00000450613.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

Genes affected

ENSG00000248752 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450613.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248752	ENST00000450613.2	TSL:3	n.71+54845A>G		intron	N/A
	ENSG00000248752	ENST00000651847.1		n.77-29657A>G		intron	N/A
	ENSG00000248752	ENST00000781629.1		n.175-29657A>G		intron	N/A

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

African (AFR) AF: 0.974 AC: 40456 AN: 41540

American (AMR) AF: 0.876 AC: 13407 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3036 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5172 AN: 5176

South Asian (SAS) AF: 0.952 AC: 4584 AN: 4816

European-Finnish (FIN) AF: 0.853 AC: 9052 AN: 10606

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58261 AN: 68014

Other (OTH) AF: 0.891 AC: 1881 AN: 2110

Alfa AF: 0.877 Hom.: 7303

Bravo AF: 0.903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs268147;

hg19: chr5-125560579;