chr4-106906844-T-C

Variant names:

• chr4-106906844-T-C
• rs427983
• ENST00000650850.1:n.486-4214T>C

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.486-4214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,982 control chromosomes in the GnomAD database, including 7,948 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 0.32 (7948 hom., cov: 31)
• Consequence: ENSG00000286147 ENST00000650850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869
• Publications: 4 publications found

Genes affected

ENSG00000286147 (HGNC:58864):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650850.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286147	ENST00000650850.1		n.486-4214T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48251 AN: 151864 Hom.: 7938 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.318 AC: 48303 AN: 151982 Hom.: 7948 Cov.: 31 AF XY: 0.312 AC XY: 23187 AN XY: 74278

African (AFR) AF: 0.393 AC: 16265 AN: 41436

American (AMR) AF: 0.240 AC: 3666 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1313 AN: 5150

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4816

European-Finnish (FIN) AF: 0.282 AC: 2987 AN: 10576

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20901 AN: 67980

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.285 Hom.: 4388

Bravo AF: 0.317

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	17
DANN	Benign	0.65
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs427983; hg19: chr4-107828001;