4-409514-A-G

Position:

• chr4-409514-A-G

Variant summary

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

The ENST00000631198.1(ENSG00000281016):​n.138+23203A>G 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 0.255 in 152,068 control chromosomes in the GnomAD database, including 5,017 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 0.25 (5017 hom., cov: 32)
• Consequence: ENST00000631198.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000631198.1	n.138+23203A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38707 AN: 151950 Hom.: 5017 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.255 AC: 38721 AN: 152068 Hom.: 5017 Cov.: 32 AF XY: 0.258 AC XY: 19140 AN XY: 74328

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.275

Alfa AF: 0.265 Hom.: 666

Bravo AF: 0.246

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11735008; hg19: chr4-403303;