5-40424324-A-C

Position:

• chr5-40424324-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000691408.1(ENSG00000283286):​n.187-5608A>C variant causes a intron, non coding transcript 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: ENST00000691408.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691408.1	n.187-5608A>C		intron_variant, non_coding_transcript_variant
	ENST00000637776.1	n.63-5608A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.581

Alfa AF: 0.576 Hom.: 29253

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6896969; hg19: chr5-40424426;