chr4-145463623-G-T

Position:

• chr4-145463623-G-T

Variant summary

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

The ENST00000658284.1(ENSG00000286420):​n.254+4856C>A 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 0.303 in 152,004 control chromosomes in the GnomAD database, including 8,967 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 (8967 hom., cov: 31)
• Consequence: ENST00000658284.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 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
	ENST00000658284.1	n.254+4856C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46074 AN: 151886 Hom.: 8965 Cov.: 31

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0984

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.303 AC: 46073 AN: 152004 Hom.: 8967 Cov.: 31 AF XY: 0.300 AC XY: 22288 AN XY: 74262

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0976

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.303

Alfa AF: 0.378 Hom.: 7664

Bravo AF: 0.275

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1866179; hg19: chr4-146384775;