chr5-148825809-A-G

Variant names:

• chr5-148825809-A-G
• rs2053044
• ENST00000798472.1:n.376+512A>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+512A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,046 control chromosomes in the GnomAD database, including 27,782 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 (27775 hom., cov: 32)
  • Exomes 𝑓: 0.59 (7 hom.)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 34 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=-0.84).
• 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303969	ENST00000798472.1		n.376+512A>G		intron	N/A
	ENSG00000303969	ENST00000798473.1		n.349+512A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91077 AN: 151896 Hom.: 27756 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.627

GnomAD4 exome AF: 0.594 AC: 19 AN: 32 Hom.: 7 Cov.: 0 AF XY: 0.654 AC XY: 17 AN XY: 26

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 9 AN: 18

Other (OTH) AF: 0.750 AC: 6 AN: 8

GnomAD4 genome AF: 0.600 AC: 91141 AN: 152014 Hom.: 27775 Cov.: 32 AF XY: 0.607 AC XY: 45098 AN XY: 74302

African (AFR) AF: 0.564 AC: 23378 AN: 41432

American (AMR) AF: 0.713 AC: 10904 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3842 AN: 5142

South Asian (SAS) AF: 0.744 AC: 3582 AN: 4816

European-Finnish (FIN) AF: 0.632 AC: 6690 AN: 10578

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

European-Non Finnish (NFE) AF: 0.567 AC: 38549 AN: 67966

Other (OTH) AF: 0.633 AC: 1336 AN: 2112

Alfa AF: 0.579 Hom.: 46094

Bravo AF: 0.601

Asia WGS AF: 0.754 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.67
PhyloP100		-0.86

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: rs2053044; hg19: chr5-148205372;