rs1408298

Variant names:

• chr6-17091063-T-C
• rs1408298
• ENST00000798149.1:n.225+3083A>G

Variant summary

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

The ENST00000798149.1(ENSG00000287359):​n.225+3083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,088 control chromosomes in the GnomAD database, including 4,131 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 0.22 (4131 hom., cov: 32)
• Consequence: ENSG00000287359 ENST00000798149.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 0 publications found

Genes affected

ENSG00000287359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287359	ENST00000798149.1	n.225+3083A>G		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798150.1	n.61+3083A>G		intron_variant	Intron 1 of 2
ENSG00000287359	ENST00000798151.1	n.211+3083A>G		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798152.1	n.207+3083A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33541 AN: 151970 Hom.: 4126 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.221 AC: 33557 AN: 152088 Hom.: 4131 Cov.: 32 AF XY: 0.219 AC XY: 16293 AN XY: 74328

African (AFR) AF: 0.121 AC: 5013 AN: 41536

American (AMR) AF: 0.166 AC: 2532 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5164

South Asian (SAS) AF: 0.189 AC: 913 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3309 AN: 10560

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18966 AN: 67948

Other (OTH) AF: 0.208 AC: 438 AN: 2110

Alfa AF: 0.249 Hom.: 596

Bravo AF: 0.205

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs1408298; hg19: chr6-17091294;