19-29662928-T-C

Variant names:

• chr19-29662928-T-C
• rs6509542
• ENST00000769873.1:n.148+1104A>G

Variant summary

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

The ENST00000769873.1(ENSG00000300186):​n.148+1104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,210 control chromosomes in the GnomAD database, including 44,002 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 0.75 (44002 hom., cov: 33)
• Consequence: ENSG00000300186 ENST00000769873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 6 publications found

Genes affected

ENSG00000300186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000769873.1. 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
	ENSG00000300186	ENST00000769873.1		n.148+1104A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114414 AN: 152092 Hom.: 43955 Cov.: 33

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.752 AC: 114519 AN: 152210 Hom.: 44002 Cov.: 33 AF XY: 0.744 AC XY: 55314 AN XY: 74396

African (AFR) AF: 0.912 AC: 37911 AN: 41578

American (AMR) AF: 0.632 AC: 9657 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2513 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2888 AN: 5144

South Asian (SAS) AF: 0.626 AC: 3015 AN: 4814

European-Finnish (FIN) AF: 0.675 AC: 7144 AN: 10590

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48978 AN: 68012

Other (OTH) AF: 0.724 AC: 1530 AN: 2112

Alfa AF: 0.727 Hom.: 20335

Bravo AF: 0.757

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.79
PhyloP100		-0.12

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: rs6509542;

hg19: chr19-30153835;