rs3093001

Variant names:

• chr6-167140697-A-C
• rs3093001
• ENST00000832763.1:n.165+330T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-167140697-A-C
• chr6-167140697-A-G
• chr6-167140697-A-T

Variant summary

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

The ENST00000832763.1(ENSG00000308245):​n.165+330T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,880 control chromosomes in the GnomAD database, including 15,967 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 0.44 (15967 hom., cov: 33)
• Consequence: ENSG00000308245 ENST00000832763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 7 publications found

Genes affected

ENSG00000308245 (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 (AMR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267970	XR_002956379.2	n.326-162T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308245	ENST00000832763.1	n.165+330T>G		intron_variant	Intron 1 of 1
ENSG00000308245	ENST00000832764.1	n.203-162T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66122 AN: 151762 Hom.: 15963 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.436 AC: 66154 AN: 151880 Hom.: 15967 Cov.: 33 AF XY: 0.441 AC XY: 32698 AN XY: 74222

African (AFR) AF: 0.212 AC: 8806 AN: 41494

American (AMR) AF: 0.599 AC: 9151 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1799 AN: 3466

East Asian (EAS) AF: 0.547 AC: 2817 AN: 5150

South Asian (SAS) AF: 0.572 AC: 2756 AN: 4814

European-Finnish (FIN) AF: 0.487 AC: 5127 AN: 10518

Middle Eastern (MID) AF: 0.531 AC: 154 AN: 290

European-Non Finnish (NFE) AF: 0.502 AC: 34078 AN: 67872

Other (OTH) AF: 0.462 AC: 973 AN: 2108

Alfa AF: 0.487 Hom.: 26924

Bravo AF: 0.434

Asia WGS AF: 0.546 AC: 1896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs3093001; hg19: chr6-167554185;