5-176707401-C-T

Variant names:

• chr5-176707401-C-T
• rs4868699
• ENST00000507236.1:n.533G>A

Variant summary

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

The ENST00000507236.1(ENSG00000248484):​n.533G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,292 control chromosomes in the GnomAD database, including 59,545 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 0.88 (59542 hom., cov: 33)
  • Exomes 𝑓: 0.88 (3 hom.)
• Consequence: ENSG00000248484 ENST00000507236.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 2 publications found

Genes affected

ENSG00000248484 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507236.1. 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
	ENSG00000248484	ENST00000507236.1	TSL:4	n.533G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000310042	ENST00000846731.1		n.201-2053C>T		intron	N/A
	ENSG00000310042	ENST00000846732.1		n.405-2053C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134439 AN: 152166 Hom.: 59503 Cov.: 33

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.874

GnomAD4 exome AF: 0.875 AC: 7 AN: 8 Hom.: 3 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 4 AN: 4

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.883 AC: 134532 AN: 152284 Hom.: 59542 Cov.: 33 AF XY: 0.880 AC XY: 65482 AN XY: 74452

African (AFR) AF: 0.912 AC: 37910 AN: 41556

American (AMR) AF: 0.827 AC: 12643 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.802 AC: 4157 AN: 5186

South Asian (SAS) AF: 0.834 AC: 4021 AN: 4824

European-Finnish (FIN) AF: 0.894 AC: 9483 AN: 10604

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60566 AN: 68030

Other (OTH) AF: 0.868 AC: 1834 AN: 2112

Alfa AF: 0.884 Hom.: 33551

Bravo AF: 0.879

Asia WGS AF: 0.825 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.56
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4868699; hg19: chr5-176134402;