4-106906844-T-C

Position:

• chr4-106906844-T-C

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.486-4214T>C variant causes a intron, non coding transcript 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: ENST00000650850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650850.1	n.486-4214T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.323

Alfa AF: 0.275 Hom.: 2801

Bravo AF: 0.317

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs427983; hg19: chr4-107828001;