4-174379628-T-C

Variant names:

• chr4-174379628-T-C
• rs6852435
• ENST00000829383.1:n.107+74T>C

Variant summary

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

The ENST00000829383.1(ENSG00000307851):​n.107+74T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,146 control chromosomes in the GnomAD database, including 2,494 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 0.17 (2494 hom., cov: 32)
• Consequence: ENSG00000307851 ENST00000829383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 8 publications found

Genes affected

ENSG00000307851 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829383.1. 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
	ENSG00000307851	ENST00000829383.1		n.107+74T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25276 AN: 152028 Hom.: 2493 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.166 AC: 25289 AN: 152146 Hom.: 2494 Cov.: 32 AF XY: 0.166 AC XY: 12340 AN XY: 74380

African (AFR) AF: 0.182 AC: 7543 AN: 41518

American (AMR) AF: 0.180 AC: 2752 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 616 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2621 AN: 5146

South Asian (SAS) AF: 0.108 AC: 522 AN: 4822

European-Finnish (FIN) AF: 0.110 AC: 1162 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9566 AN: 67978

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.159 Hom.: 5428

Bravo AF: 0.175

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.57
PhyloP100		-1.3

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: rs6852435;

hg19: chr4-175300779;