chr5-40424324-A-C

Variant names:

• chr5-40424324-A-C
• rs6896969
• ENST00000637776.2:n.360-5608A>C

Variant summary

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

The ENST00000637776.2(ENSG00000283286):​n.360-5608A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 152,064 control chromosomes in the GnomAD database, including 25,134 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 (25134 hom., cov: 32)
• Consequence: ENSG00000283286 ENST00000637776.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 37 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=-0.98).
• 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	ENST00000637776.2	n.360-5608A>C		intron_variant	Intron 1 of 1	5
ENSG00000283286	ENST00000691408.1	n.187-5608A>C		intron_variant	Intron 1 of 1
ENSG00000283286	ENST00000809813.1	n.459+653A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86170 AN: 151946 Hom.: 25119 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.567 AC: 86229 AN: 152064 Hom.: 25134 Cov.: 32 AF XY: 0.560 AC XY: 41613 AN XY: 74322

African (AFR) AF: 0.611 AC: 25326 AN: 41462

American (AMR) AF: 0.472 AC: 7211 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2121 AN: 3468

East Asian (EAS) AF: 0.143 AC: 738 AN: 5174

South Asian (SAS) AF: 0.467 AC: 2257 AN: 4830

European-Finnish (FIN) AF: 0.542 AC: 5716 AN: 10554

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

European-Non Finnish (NFE) AF: 0.602 AC: 40898 AN: 67974

Other (OTH) AF: 0.581 AC: 1228 AN: 2114

Alfa AF: 0.580 Hom.: 47368

Bravo AF: 0.560

Asia WGS AF: 0.373 AC: 1295 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.63
DANN	Benign	0.65
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6896969; hg19: chr5-40424426;