rs4885678

Variant names:

• chr13-79866356-G-T
• rs4885678
• ENST00000780129.1:n.129-1131C>A

Variant summary

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

The ENST00000780129.1(ENSG00000301598):​n.129-1131C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,970 control chromosomes in the GnomAD database, including 2,874 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 0.19 (2874 hom., cov: 32)
• Consequence: ENSG00000301598 ENST00000780129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 1 publications found

Genes affected

ENSG00000301598 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780129.1. 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
	ENSG00000301598	ENST00000780129.1		n.129-1131C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28399 AN: 151848 Hom.: 2877 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.187 AC: 28420 AN: 151970 Hom.: 2874 Cov.: 32 AF XY: 0.186 AC XY: 13832 AN XY: 74292

African (AFR) AF: 0.261 AC: 10809 AN: 41444

American (AMR) AF: 0.218 AC: 3324 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3466

East Asian (EAS) AF: 0.283 AC: 1458 AN: 5154

South Asian (SAS) AF: 0.190 AC: 915 AN: 4822

European-Finnish (FIN) AF: 0.0805 AC: 852 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9996 AN: 67940

Other (OTH) AF: 0.189 AC: 398 AN: 2110

Alfa AF: 0.157 Hom.: 1192

Bravo AF: 0.201

Asia WGS AF: 0.238 AC: 828 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	0.41
DANN	Benign	0.50
PhyloP100		-0.42

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: rs4885678;

hg19: chr13-80440491;