chr3-161674788-C-G

Variant names:

• chr3-161674788-C-G
• rs6808138
• ENST00000665274.1:n.116-59654C>G

Variant summary

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

The ENST00000665274.1(ENSG00000288087):​n.116-59654C>G 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 152,024 control chromosomes in the GnomAD database, including 2,838 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 (2838 hom., cov: 32)
• Consequence: ENSG00000288087 ENST00000665274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767

Genes affected

ENSG00000288087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 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
ENSG00000288087	ENST00000665274.1	n.116-59654C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27869 AN: 151906 Hom.: 2830 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.184 AC: 27910 AN: 152024 Hom.: 2838 Cov.: 32 AF XY: 0.185 AC XY: 13774 AN XY: 74298

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.0895

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.189

Alfa AF: 0.142 Hom.: 927

Bravo AF: 0.193

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6808138; hg19: chr3-161392576;