rs10516537

chr4-106706914-A-Cchr4-106706914-A-G

Variant summary

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

The ENST00000650850.1(ENSG00000286147):n.319-424A>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 0.844 in 152,026 control chromosomes in the GnomAD database, including 54,345 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 0.84 (54345 hom., cov: 31)
• Consequence: ENST00000650850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377356	XR_939051.1	n.261-424A>C		intron_variant, non_coding_transcript_variant
LOC105377356	XR_939053.3	n.261-424A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650850.1	n.319-424A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128201 AN: 151908 Hom.: 54316 Cov.: 31

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.844 AC: 128279 AN: 152026 Hom.: 54345 Cov.: 31 AF XY: 0.850 AC XY: 63209 AN XY: 74320

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.853

Alfa AF: 0.853 Hom.: 66235

Bravo AF: 0.841

Asia WGS AF: 0.885 AC: 3073 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516537; hg19: chr4-107628071;