rs7186852

Positions:

• chr16-30624338-A-G

Variant summary

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

The ENST00000568120.1(ENSG00000261680):​n.377T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,124 control chromosomes in the GnomAD database, including 18,720 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 0.46 (18714 hom., cov: 32)
  • Exomes 𝑓: 0.44 (6 hom.)
• Consequence: ENST00000568120.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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
	ENST00000568120.1	n.377T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69779 AN: 151956 Hom.: 18692 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.412

GnomAD4 exome AF: 0.440 AC: 22 AN: 50 Hom.: 6 Cov.: 0 AF XY: 0.406 AC XY: 13 AN XY: 32

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.667

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.459 AC: 69839 AN: 152074 Hom.: 18714 Cov.: 32 AF XY: 0.458 AC XY: 34009 AN XY: 74334

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.413

Alfa AF: 0.361 Hom.: 21139

Bravo AF: 0.458

Asia WGS AF: 0.464 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7186852; hg19: chr16-30635659;