6-466033-C-T

Variant names:

• chr6-466033-C-T
• rs1540771
• ENST00000661640.1:n.336-9175C>T

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.336-9175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,088 control chromosomes in the GnomAD database, including 14,072 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 0.40 (14072 hom., cov: 33)
• Consequence: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 49 publications found

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661640.1. 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
	ENSG00000286364	ENST00000661640.1		n.336-9175C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61020 AN: 151966 Hom.: 14070 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.401 AC: 61043 AN: 152088 Hom.: 14072 Cov.: 33 AF XY: 0.398 AC XY: 29608 AN XY: 74344

African (AFR) AF: 0.171 AC: 7084 AN: 41498

American (AMR) AF: 0.498 AC: 7604 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1671 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5172

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4820

European-Finnish (FIN) AF: 0.475 AC: 5014 AN: 10556

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35233 AN: 67982

Other (OTH) AF: 0.438 AC: 925 AN: 2114

Alfa AF: 0.473 Hom.: 55215

Bravo AF: 0.394

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.52
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1540771; hg19: chr6-466033;