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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901238	XR_007059398.1	n.128-107G>T		intron_variant	Intron 1 of 2
LOC124901238	XR_007059399.1	n.128-107G>T		intron_variant	Intron 1 of 3
LOC124901238	XR_007059400.1	n.128-107G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305114	ENST00000808839.1	n.83-107G>T		intron_variant	Intron 1 of 4
ENSG00000305114	ENST00000808840.1	n.283+8279G>T		intron_variant	Intron 2 of 2
ENSG00000305114	ENST00000808841.1	n.138-107G>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs9405484; hg19: chr6-1498457;