rs78416326

Variant names:

• chr3-170356729-G-C
• rs78416326
• ENST00000727606.1:n.103C>G

Variant summary

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

The ENST00000727606.1(ENSG00000295042):​n.103C>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 0.158 in 151,758 control chromosomes in the GnomAD database, including 2,383 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 0.16 (2383 hom., cov: 30)
• Consequence: ENSG00000295042 ENST00000727606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.909
• Publications: 10 publications found

Genes affected

ENSG00000295042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727606.1. 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
	ENSG00000295042	ENST00000727606.1		n.103C>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23905 AN: 151638 Hom.: 2376 Cov.: 30

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.158 AC: 23919 AN: 151758 Hom.: 2383 Cov.: 30 AF XY: 0.160 AC XY: 11867 AN XY: 74196

African (AFR) AF: 0.0403 AC: 1674 AN: 41510

American (AMR) AF: 0.241 AC: 3681 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 754 AN: 3464

East Asian (EAS) AF: 0.220 AC: 1130 AN: 5136

South Asian (SAS) AF: 0.0717 AC: 345 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2156 AN: 10484

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13569 AN: 67770

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.171 Hom.: 311

Bravo AF: 0.157

Asia WGS AF: 0.153 AC: 532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	14
DANN	Benign	0.64
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs78416326; hg19: chr3-170074517;