19-4007082-T-C

Variant names:

• chr19-4007082-T-C
• rs735842
• ENST00000812314.1:n.160A>G

Variant summary

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

The ENST00000812314.1(ENSG00000305677):​n.160A>G 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 0.212 in 148,982 control chromosomes in the GnomAD database, including 3,576 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 0.21 (3576 hom., cov: 31)
• Consequence: ENSG00000305677 ENST00000812314.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 15 publications found

Genes affected

ENSG00000305677 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812314.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305677	ENST00000812314.1		n.160A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 31585 AN: 148858 Hom.: 3577 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.212 AC: 31594 AN: 148982 Hom.: 3576 Cov.: 31 AF XY: 0.211 AC XY: 15332 AN XY: 72654

African (AFR) AF: 0.293 AC: 12023 AN: 40980

American (AMR) AF: 0.163 AC: 2442 AN: 15020

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 769 AN: 3424

East Asian (EAS) AF: 0.0261 AC: 125 AN: 4788

South Asian (SAS) AF: 0.128 AC: 581 AN: 4538

European-Finnish (FIN) AF: 0.234 AC: 2347 AN: 10026

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12666 AN: 66952

Other (OTH) AF: 0.224 AC: 467 AN: 2084

Alfa AF: 0.193 Hom.: 11063

Bravo AF: 0.210

Asia WGS AF: 0.0980 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.063
DANN	Benign	0.44
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs735842;

hg19: chr19-4007080;