3-166274777-C-T

Variant names:

• chr3-166274777-C-T
• rs638557
• ENST00000781051.1:n.227-8705C>T

Variant summary

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

The ENST00000781051.1(ENSG00000301714):​n.227-8705C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,866 control chromosomes in the GnomAD database, including 37,671 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 0.70 (37671 hom., cov: 32)
• Consequence: ENSG00000301714 ENST00000781051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.41
• Publications: 3 publications found

Genes affected

ENSG00000301714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 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
ENSG00000301714	ENST00000781051.1	n.227-8705C>T		intron_variant	Intron 1 of 1
ENSG00000301714	ENST00000781052.1	n.227-8708C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106545 AN: 151746 Hom.: 37633 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.702 AC: 106643 AN: 151866 Hom.: 37671 Cov.: 32 AF XY: 0.709 AC XY: 52610 AN XY: 74220

African (AFR) AF: 0.750 AC: 31131 AN: 41506

American (AMR) AF: 0.662 AC: 10097 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2091 AN: 3460

East Asian (EAS) AF: 0.703 AC: 3619 AN: 5148

South Asian (SAS) AF: 0.765 AC: 3688 AN: 4822

European-Finnish (FIN) AF: 0.799 AC: 8446 AN: 10566

Middle Eastern (MID) AF: 0.638 AC: 185 AN: 290

European-Non Finnish (NFE) AF: 0.671 AC: 45523 AN: 67802

Other (OTH) AF: 0.668 AC: 1410 AN: 2112

Alfa AF: 0.702 Hom.: 4864

Bravo AF: 0.691

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.81
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs638557; hg19: chr3-165992565;