16-58868114-C-G

Position:

• chr16-58868114-C-G

Variant summary

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

The ENST00000657379.1(ENSG00000245768):​n.650+111936C>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 0.251 in 151,890 control chromosomes in the GnomAD database, including 6,687 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 0.25 (6687 hom., cov: 31)
• Consequence: ENST00000657379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371296	XR_933639.3	n.237+11871G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657379.1	n.650+111936C>G		intron_variant, non_coding_transcript_variant
	ENST00000662590.1	n.237+11871G>C		intron_variant, non_coding_transcript_variant
	ENST00000500117.1	n.679+111936C>G		intron_variant, non_coding_transcript_variant		2
	ENST00000569328.2	n.323+11765G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38083 AN: 151772 Hom.: 6653 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.251 AC: 38167 AN: 151890 Hom.: 6687 Cov.: 31 AF XY: 0.247 AC XY: 18370 AN XY: 74256

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.274

Alfa AF: 0.199 Hom.: 538

Bravo AF: 0.278

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4784993; hg19: chr16-58902018;