16-30624338-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

Genes affected

ENSG00000261680 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568120.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261680	ENST00000568120.1	TSL:6	n.377T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000260167	ENST00000761153.1		n.191-866A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.667 AC: 8 AN: 12

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.400 AC: 12 AN: 30

Other (OTH) AF: 0.333 AC: 2 AN: 6

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

African (AFR) AF: 0.731 AC: 30340 AN: 41482

American (AMR) AF: 0.326 AC: 4986 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3468

East Asian (EAS) AF: 0.114 AC: 590 AN: 5182

South Asian (SAS) AF: 0.697 AC: 3353 AN: 4808

European-Finnish (FIN) AF: 0.324 AC: 3423 AN: 10572

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24630 AN: 67950

Other (OTH) AF: 0.413 AC: 871 AN: 2110

Alfa AF: 0.379 Hom.: 52716

Bravo AF: 0.458

Asia WGS AF: 0.464 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.67
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs7186852; hg19: chr16-30635659;