chr5-40412364-A-G

Variant names:

• chr5-40412364-A-G
• rs6888952
• ENST00000691408.1:n.186+968A>G

Variant summary

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

The ENST00000691408.1(ENSG00000283286):​n.186+968A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,912 control chromosomes in the GnomAD database, including 25,423 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 0.57 (25423 hom., cov: 31)
• Consequence: ENSG00000283286 ENST00000691408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 7 publications found

Genes affected

ENSG00000283286 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 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
ENSG00000283286	ENST00000691408.1	n.186+968A>G		intron_variant	Intron 1 of 1
ENSG00000283286	ENST00000809813.1	n.213+968A>G		intron_variant	Intron 1 of 3
ENSG00000283286	ENST00000809814.1	n.188+968A>G		intron_variant	Intron 1 of 2
ENSG00000305258	ENST00000809861.1	n.238+503T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86582 AN: 151794 Hom.: 25408 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.570 AC: 86641 AN: 151912 Hom.: 25423 Cov.: 31 AF XY: 0.563 AC XY: 41775 AN XY: 74244

African (AFR) AF: 0.612 AC: 25308 AN: 41384

American (AMR) AF: 0.474 AC: 7243 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3468

East Asian (EAS) AF: 0.143 AC: 737 AN: 5162

South Asian (SAS) AF: 0.470 AC: 2266 AN: 4826

European-Finnish (FIN) AF: 0.543 AC: 5715 AN: 10530

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41156 AN: 67958

Other (OTH) AF: 0.580 AC: 1221 AN: 2104

Alfa AF: 0.594 Hom.: 3461

Bravo AF: 0.564

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.44
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6888952; hg19: chr5-40412466;