rs4956263

chr4-106670493-T-G

Variant summary

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

The ENST00000650850.1(ENSG00000286147):n.318+28479T>G 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 0.0838 in 152,216 control chromosomes in the GnomAD database, including 667 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 0.084 (667 hom., cov: 32)
• Consequence: ENST00000650850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377356	XR_939051.1	n.260+28479T>G		intron_variant, non_coding_transcript_variant
LOC105377356	XR_939053.3	n.260+28479T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650850.1	n.318+28479T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12766 AN: 152098 Hom.: 666 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0670

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0838 AC: 12760 AN: 152216 Hom.: 667 Cov.: 32 AF XY: 0.0839 AC XY: 6246 AN XY: 74402

Gnomad4 AFR AF: 0.0215

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.0670

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0808

Alfa AF: 0.104 Hom.: 821

Bravo AF: 0.0756

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4956263; hg19: chr4-107591650;