chr4-106915154-A-G

Variant names:

• chr4-106915154-A-G
• rs429941
• ENST00000650850.1:n.639+512A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650850.1(ENSG00000286147):​n.639+512A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000286147 ENST00000650850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 3 publications found

Genes affected

ENSG00000286147 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286147	ENST00000650850.1	n.639+512A>G		intron_variant	Intron 8 of 10

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

African (AFR) AF: 0.396 AC: 16420 AN: 41504

American (AMR) AF: 0.220 AC: 3360 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1319 AN: 5166

South Asian (SAS) AF: 0.217 AC: 1049 AN: 4834

European-Finnish (FIN) AF: 0.294 AC: 3114 AN: 10580

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20269 AN: 67960

Other (OTH) AF: 0.296 AC: 623 AN: 2108

Alfa AF: 0.236 Hom.: 813

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
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs429941; hg19: chr4-107836311;