ENST00000651847.1:n.308-29422T>G

Variant names:

• chr5-126038049-A-C
• rs1175307
• ENST00000651847.1:n.308-29422T>G

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.308-29422T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.985 in 152,258 control chromosomes in the GnomAD database, including 73,853 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 0.98 (73853 hom., cov: 32)
• Consequence: ENSG00000248752 ENST00000651847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1774+59958T>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000651847.1	n.308-29422T>G		intron_variant	Intron 3 of 15
ENSG00000248752	ENST00000781630.1	n.156-29422T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.985 AC: 149839 AN: 152140 Hom.: 73792 Cov.: 32

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.986

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.985 AC: 149959 AN: 152258 Hom.: 73853 Cov.: 32 AF XY: 0.985 AC XY: 73364 AN XY: 74452

African (AFR) AF: 0.996 AC: 41378 AN: 41558

American (AMR) AF: 0.986 AC: 15061 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3339 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5181 AN: 5182

South Asian (SAS) AF: 0.979 AC: 4725 AN: 4824

European-Finnish (FIN) AF: 0.997 AC: 10593 AN: 10620

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66479 AN: 68010

Other (OTH) AF: 0.975 AC: 2057 AN: 2110

Alfa AF: 0.979 Hom.: 9054

Bravo AF: 0.985

Asia WGS AF: 0.991 AC: 3444 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1175307; hg19: chr5-125373742;