chr4-6889708-G-A

Variant names:

• chr4-6889708-G-A
• rs11734099
• ENST00000779681.1:n.629+5135C>T

Variant summary

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

The ENST00000779681.1(ENSG00000301554):​n.629+5135C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,226 control chromosomes in the GnomAD database, including 2,487 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 0.15 (2487 hom., cov: 33)
• Consequence: ENSG00000301554 ENST00000779681.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 9 publications found

Genes affected

ENSG00000301554 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779681.1. 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
	ENSG00000301554	ENST00000779681.1		n.629+5135C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22885 AN: 152110 Hom.: 2486 Cov.: 33

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.150 AC: 22878 AN: 152226 Hom.: 2487 Cov.: 33 AF XY: 0.152 AC XY: 11333 AN XY: 74400

African (AFR) AF: 0.0370 AC: 1539 AN: 41574

American (AMR) AF: 0.192 AC: 2938 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2869 AN: 5160

South Asian (SAS) AF: 0.160 AC: 773 AN: 4830

European-Finnish (FIN) AF: 0.193 AC: 2043 AN: 10594

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11842 AN: 67980

Other (OTH) AF: 0.157 AC: 332 AN: 2110

Alfa AF: 0.164 Hom.: 777

Bravo AF: 0.150

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.14
DANN	Benign	0.86
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11734099; hg19: chr4-6891435;