rs1084651

Variant names:

• chr6-160668785-G-A
• rs1084651
• ENST00000452651.1:n.115-2412C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000452651.1(ENSG00000243831):​n.115-2412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 150,458 control chromosomes in the GnomAD database, including 4,704 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 0.24 (4704 hom., cov: 30)
• Consequence: ENSG00000243831 ENST00000452651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

ENSG00000243831 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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
ENSG00000243831	ENST00000452651.1	n.115-2412C>T		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35382 AN: 150372 Hom.: 4698 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0742

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.235 AC: 35406 AN: 150458 Hom.: 4704 Cov.: 30 AF XY: 0.239 AC XY: 17550 AN XY: 73440

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.211

Alfa AF: 0.185 Hom.: 4937

Asia WGS AF: 0.371 AC: 1287 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	2.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1084651; hg19: chr6-161089817;