6-1498222-G-T

Variant names:

• chr6-1498222-G-T
• rs9405484
• ENST00000808839.1:n.83-107G>T

Variant summary

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

The ENST00000808839.1(ENSG00000305114):​n.83-107G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,144 control chromosomes in the GnomAD database, including 3,354 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 0.18 (3354 hom., cov: 32)
• Consequence: ENSG00000305114 ENST00000808839.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 3 publications found

Genes affected

ENSG00000305114 (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 (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808839.1. 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
	ENSG00000305114	ENST00000808839.1		n.83-107G>T		intron	N/A
	ENSG00000305114	ENST00000808840.1		n.283+8279G>T		intron	N/A
	ENSG00000305114	ENST00000808841.1		n.138-107G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28060 AN: 152026 Hom.: 3352 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.184 AC: 28067 AN: 152144 Hom.: 3354 Cov.: 32 AF XY: 0.189 AC XY: 14051 AN XY: 74378

African (AFR) AF: 0.109 AC: 4540 AN: 41516

American (AMR) AF: 0.185 AC: 2835 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3468

East Asian (EAS) AF: 0.609 AC: 3142 AN: 5156

South Asian (SAS) AF: 0.363 AC: 1747 AN: 4812

European-Finnish (FIN) AF: 0.179 AC: 1895 AN: 10610

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12757 AN: 67984

Other (OTH) AF: 0.216 AC: 454 AN: 2104

Alfa AF: 0.193 Hom.: 13446

Bravo AF: 0.183

Asia WGS AF: 0.427 AC: 1485 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	2.0
DANN	Benign	0.61
PhyloP100		0.079

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: rs9405484;

hg19: chr6-1498457;