NM_001396016.1:c.-19-3838C>A

Variant names:

• chr19-52664681-G-T
• rs12976870
• NM_001396016.1:c.-19-3838C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001396016.1(LOC122539214):​c.-19-3838C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 148,578 control chromosomes in the GnomAD database, including 942 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 0.11 (942 hom., cov: 28)
• Consequence: LOC122539214 NM_001396016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• Publications: 4 publications found

Genes affected

LOC122539214 (HGNC:0):

ENSG00000269825 (HGNC:):

ZNF83 (HGNC:13158): (zinc finger protein 83) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC122539214	NM_001396016.1	MANE Select	c.-19-3838C>A		intron	N/A	NP_001382945.1	A0A7P0TAN4
	ZNF83	NM_001277945.2		c.-657-3838C>A		intron	N/A	NP_001264874.1	P51522-1
	ZNF83	NM_001277946.2		c.-442-3838C>A		intron	N/A	NP_001264875.1	P51522-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000269825	ENST00000598322.3	TSL:6 MANE Select	c.-19-3838C>A		intron	N/A	ENSP00000506273.1	A0A7P0TAN4
	ENSG00000269825	ENST00000963676.1		c.-20+1785C>A		intron	N/A	ENSP00000633735.1
	ENSG00000269825	ENST00000963677.1		c.-209+1149C>A		intron	N/A	ENSP00000633736.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 15977 AN: 148448 Hom.: 941 Cov.: 28

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0695

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.000616

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0882

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.108 AC: 15989 AN: 148578 Hom.: 942 Cov.: 28 AF XY: 0.105 AC XY: 7601 AN XY: 72258

African (AFR) AF: 0.147 AC: 5975 AN: 40542

American (AMR) AF: 0.0768 AC: 1126 AN: 14664

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 280 AN: 3442

East Asian (EAS) AF: 0.000617 AC: 3 AN: 4864

South Asian (SAS) AF: 0.0529 AC: 244 AN: 4614

European-Finnish (FIN) AF: 0.101 AC: 995 AN: 9882

Middle Eastern (MID) AF: 0.0915 AC: 26 AN: 284

European-Non Finnish (NFE) AF: 0.105 AC: 7098 AN: 67320

Other (OTH) AF: 0.0869 AC: 179 AN: 2060

Alfa AF: 0.101 Hom.: 457

Bravo AF: 0.107

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12976870; hg19: chr19-53167934;