5-148825489-A-G

Variant names:

• chr5-148825489-A-G
• rs2400707
• ENST00000798472.1:n.376+192A>G

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.376+192A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,036 control chromosomes in the GnomAD database, including 27,773 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 0.60 (27773 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 51 publications found

Genes affected

ENSG00000303969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798472.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303969	ENST00000798472.1		n.376+192A>G		intron	N/A
	ENSG00000303969	ENST00000798473.1		n.349+192A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91077 AN: 151916 Hom.: 27754 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.627

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

⚠️ 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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

⚠️ 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: 0.599 AC: 91141 AN: 152034 Hom.: 27773 Cov.: 32 AF XY: 0.607 AC XY: 45107 AN XY: 74328

African (AFR) AF: 0.564 AC: 23381 AN: 41436

American (AMR) AF: 0.712 AC: 10874 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2137 AN: 3466

East Asian (EAS) AF: 0.746 AC: 3856 AN: 5166

South Asian (SAS) AF: 0.743 AC: 3585 AN: 4826

European-Finnish (FIN) AF: 0.632 AC: 6678 AN: 10566

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38569 AN: 67984

Other (OTH) AF: 0.633 AC: 1335 AN: 2110

Alfa AF: 0.582 Hom.: 52699

Bravo AF: 0.601

Asia WGS AF: 0.750 AC: 2605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.25
PhyloP100		-0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2400707; hg19: chr5-148205052;