chr4-22130408-G-C

Position:

• chr4-22130408-G-C

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.859+28778G>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 0.3 in 151,990 control chromosomes in the GnomAD database, including 7,069 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 0.30 (7069 hom., cov: 32)
• Consequence: ENST00000510705.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 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
	ENST00000510705.3	n.859+28778G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45599 AN: 151872 Hom.: 7061 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.300 AC: 45647 AN: 151990 Hom.: 7069 Cov.: 32 AF XY: 0.303 AC XY: 22508 AN XY: 74274

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.309

Alfa AF: 0.181 Hom.: 360

Bravo AF: 0.297

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9992275; hg19: chr4-22132031;