rs7186852

Variant names:

• chr16-30624338-A-G
• rs7186852
• ENST00000568120.1:n.377T>C

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: ENSG00000261680 ENST00000568120.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

ENSG00000261680 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261680	ENST00000568120.1	n.377T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;