4-154980451-A-G

Position:

• chr4-154980451-A-G

Variant summary

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

The variant allele was found at a frequency of 0.666 in 152,028 control chromosomes in the GnomAD database, including 35,383 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 0.67 (35383 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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 (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.154980451A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101127 AN: 151912 Hom.: 35324 Cov.: 33

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.666 AC: 101237 AN: 152028 Hom.: 35383 Cov.: 33 AF XY: 0.666 AC XY: 49478 AN XY: 74296

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.632

Alfa AF: 0.640 Hom.: 5726

Bravo AF: 0.673

Asia WGS AF: 0.700 AC: 2431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
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: rs7687314; hg19: chr4-155901603;