5-148836839-G-A

Variant names:

• chr5-148836839-G-A
• rs6888329
• ENST00000798472.1:n.376+11542G>A

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.376+11542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 152,058 control chromosomes in the GnomAD database, including 34,069 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 0.67 (34069 hom., cov: 32)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303969	ENST00000798472.1	n.376+11542G>A		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1	n.349+11542G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101154 AN: 151938 Hom.: 34028 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.666 AC: 101241 AN: 152058 Hom.: 34069 Cov.: 32 AF XY: 0.662 AC XY: 49240 AN XY: 74332

African (AFR) AF: 0.724 AC: 30007 AN: 41468

American (AMR) AF: 0.648 AC: 9899 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2015 AN: 5166

South Asian (SAS) AF: 0.628 AC: 3035 AN: 4830

European-Finnish (FIN) AF: 0.641 AC: 6774 AN: 10562

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44858 AN: 67980

Other (OTH) AF: 0.678 AC: 1431 AN: 2112

Alfa AF: 0.659 Hom.: 63160

Bravo AF: 0.664

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.27
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6888329; hg19: chr5-148216402;