rs6808138

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-161674788-C-G
• chr3-161674788-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000288087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.205 AC: 8479 AN: 41444

American (AMR) AF: 0.265 AC: 4054 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 508 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1071 AN: 5148

South Asian (SAS) AF: 0.358 AC: 1724 AN: 4820

European-Finnish (FIN) AF: 0.0895 AC: 945 AN: 10564

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10557 AN: 67978

Other (OTH) AF: 0.189 AC: 399 AN: 2112

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
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs6808138; hg19: chr3-161392576;