4-105127203-T-G

Position:

• chr4-105127203-T-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 0.744 in 152,034 control chromosomes in the GnomAD database, including 42,381 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 0.74 (42381 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105127203T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112955 AN: 151916 Hom.: 42323 Cov.: 33

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.744 AC: 113075 AN: 152034 Hom.: 42381 Cov.: 33 AF XY: 0.750 AC XY: 55699 AN XY: 74312

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.759

Alfa AF: 0.691 Hom.: 56119

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541374; hg19: chr4-106048360;