5-57648412-A-G

Variant names:

• chr5-57648412-A-G
• rs2109479
• ENST00000718447.1:n.272-16839A>G

Variant summary

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

The ENST00000718447.1(ENSG00000293693):​n.272-16839A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,000 control chromosomes in the GnomAD database, including 6,487 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 0.27 (6487 hom., cov: 32)
• Consequence: ENSG00000293693 ENST00000718447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 5 publications found

Genes affected

ENSG00000293693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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
ENSG00000293693	ENST00000718447.1	n.272-16839A>G		intron_variant	Intron 1 of 2
ENSG00000293693	ENST00000718448.1	n.264-16839A>G		intron_variant	Intron 1 of 2
ENSG00000293693	ENST00000718449.1	n.361-16839A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41111 AN: 151882 Hom.: 6460 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.271 AC: 41184 AN: 152000 Hom.: 6487 Cov.: 32 AF XY: 0.268 AC XY: 19886 AN XY: 74300

African (AFR) AF: 0.440 AC: 18234 AN: 41440

American (AMR) AF: 0.174 AC: 2651 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1650 AN: 5164

South Asian (SAS) AF: 0.154 AC: 742 AN: 4816

European-Finnish (FIN) AF: 0.251 AC: 2649 AN: 10556

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14183 AN: 67970

Other (OTH) AF: 0.239 AC: 505 AN: 2112

Alfa AF: 0.216 Hom.: 11379

Bravo AF: 0.278

Asia WGS AF: 0.213 AC: 739 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2109479; hg19: chr5-56944239;