4-166422787-A-G

Position:

• chr4-166422787-A-G

Variant summary

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

The ENST00000514134.1(ENSG00000249675):​n.206-33358T>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 0.094 in 152,200 control chromosomes in the GnomAD database, including 940 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 0.094 (940 hom., cov: 32)
• Consequence: ENST00000514134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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
	ENST00000514134.1	n.206-33358T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14288 AN: 152082 Hom.: 935 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0940 AC: 14310 AN: 152200 Hom.: 940 Cov.: 32 AF XY: 0.0952 AC XY: 7084 AN XY: 74400

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0714 Hom.: 157

Bravo AF: 0.101

Asia WGS AF: 0.204 AC: 708 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17635075; hg19: chr4-167343939;