rs3107346

Variant names:

• chr10-111501405-T-C
• rs3107346
• ENST00000829409.1:n.388A>G

Variant summary

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

The ENST00000829409.1(ENSG00000307856):​n.388A>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 0.353 in 151,886 control chromosomes in the GnomAD database, including 9,717 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 0.35 (9717 hom., cov: 31)
• Consequence: ENSG00000307856 ENST00000829409.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 1 publications found

Genes affected

ENSG00000307856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829409.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307856	ENST00000829409.1		n.388A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307876	ENST00000829553.1		n.226+19516T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53587 AN: 151768 Hom.: 9705 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.353 AC: 53647 AN: 151886 Hom.: 9717 Cov.: 31 AF XY: 0.350 AC XY: 26012 AN XY: 74226

African (AFR) AF: 0.302 AC: 12506 AN: 41420

American (AMR) AF: 0.437 AC: 6665 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3462

East Asian (EAS) AF: 0.411 AC: 2125 AN: 5166

South Asian (SAS) AF: 0.350 AC: 1680 AN: 4800

European-Finnish (FIN) AF: 0.281 AC: 2963 AN: 10550

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25171 AN: 67908

Other (OTH) AF: 0.358 AC: 756 AN: 2110

Alfa AF: 0.370 Hom.: 28845

Bravo AF: 0.365

Asia WGS AF: 0.373 AC: 1296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.51
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3107346; hg19: chr10-113261163;