6-84354740-C-T

Variant names:

• chr6-84354740-C-T
• rs1555173
• ENST00000818903.1:n.106+13988C>T

Variant summary

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

The ENST00000818903.1(ENSG00000306479):​n.106+13988C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,144 control chromosomes in the GnomAD database, including 52,975 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 0.83 (52975 hom., cov: 32)
• Consequence: ENSG00000306479 ENST00000818903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 2 publications found

Genes affected

ENSG00000306479 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818903.1. 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
	ENSG00000306479	ENST00000818903.1		n.106+13988C>T		intron	N/A
	ENSG00000306479	ENST00000818904.1		n.164+11009C>T		intron	N/A
	ENSG00000306479	ENST00000818905.1		n.158+11009C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126600 AN: 152026 Hom.: 52936 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.833 AC: 126690 AN: 152144 Hom.: 52975 Cov.: 32 AF XY: 0.834 AC XY: 62024 AN XY: 74384

African (AFR) AF: 0.753 AC: 31238 AN: 41472

American (AMR) AF: 0.868 AC: 13261 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3040 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4757 AN: 5160

South Asian (SAS) AF: 0.932 AC: 4498 AN: 4824

European-Finnish (FIN) AF: 0.834 AC: 8847 AN: 10610

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58249 AN: 68010

Other (OTH) AF: 0.848 AC: 1790 AN: 2110

Alfa AF: 0.841 Hom.: 9354

Bravo AF: 0.832

Asia WGS AF: 0.904 AC: 3146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.6
DANN	Benign	0.62
PhyloP100		0.26

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: rs1555173;

hg19: chr6-85064458;