rs4956263

Variant names:

• chr4-106670493-T-G
• rs4956263
• ENST00000650850.1:n.318+28479T>G

Variant summary

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

The ENST00000650850.1(ENSG00000286147):​n.318+28479T>G variant causes a intron 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: ENSG00000286147 ENST00000650850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 4 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=-0.88).
• 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 rank	MANE	Protein	UniProt
LOC105377356	XR_939051.1	n.260+28479T>G		intron_variant	Intron 3 of 5
LOC105377356	XR_939053.3	n.260+28479T>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286147	ENST00000650850.1	n.318+28479T>G		intron_variant	Intron 4 of 10

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

African (AFR) AF: 0.0215 AC: 894 AN: 41574

American (AMR) AF: 0.0742 AC: 1134 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0670 AC: 232 AN: 3462

East Asian (EAS) AF: 0.151 AC: 783 AN: 5172

South Asian (SAS) AF: 0.0990 AC: 478 AN: 4828

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10590

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7632 AN: 67980

Other (OTH) AF: 0.0808 AC: 171 AN: 2116

Alfa AF: 0.0939 Hom.: 1010

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
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs4956263; hg19: chr4-107591650;