rs429941

Positions:

• chr4-106915154-A-G
• chr4-106915154-A-T

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 0.312 in 152,072 control chromosomes in the GnomAD database, including 7,714 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 0.31 (7714 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.106915154A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286147	ENST00000650850.1	n.639+512A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47453 AN: 151954 Hom.: 7704 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.312 AC: 47509 AN: 152072 Hom.: 7714 Cov.: 32 AF XY: 0.308 AC XY: 22864 AN XY: 74346

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.296

Alfa AF: 0.230 Hom.: 758

Bravo AF: 0.306

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs429941; hg19: chr4-107836311;