rs3097167

Variant names:

• chr5-116789382-G-A
• rs3097167
• ENST00000835801.1:n.184-17509G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-116789382-G-A
• chr5-116789382-G-C
• chr5-116789382-G-T

Variant summary

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

The ENST00000835801.1(ENSG00000308692):​n.184-17509G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,186 control chromosomes in the GnomAD database, including 55,147 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 0.85 (55147 hom., cov: 32)
• Consequence: ENSG00000308692 ENST00000835801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• Publications: 4 publications found

Genes affected

ENSG00000308692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379133	XR_948689.3	n.149-17509G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308692	ENST00000835801.1	n.184-17509G>A		intron_variant	Intron 1 of 3
ENSG00000308692	ENST00000835802.1	n.184-17509G>A		intron_variant	Intron 1 of 4
ENSG00000308692	ENST00000835803.1	n.184-17509G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129107 AN: 152068 Hom.: 55111 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.849 AC: 129197 AN: 152186 Hom.: 55147 Cov.: 32 AF XY: 0.843 AC XY: 62746 AN XY: 74396

African (AFR) AF: 0.929 AC: 38618 AN: 41554

American (AMR) AF: 0.831 AC: 12687 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2768 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3527 AN: 5178

South Asian (SAS) AF: 0.697 AC: 3356 AN: 4814

European-Finnish (FIN) AF: 0.813 AC: 8611 AN: 10588

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56787 AN: 67998

Other (OTH) AF: 0.841 AC: 1772 AN: 2108

Alfa AF: 0.837 Hom.: 170710

Bravo AF: 0.857

Asia WGS AF: 0.735 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	7.6
DANN	Benign	0.55
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs3097167; hg19: chr5-116125078;