rs6803398

Variant names:

• chr3-965759-A-G
• rs6803398
• XR_001740585.2:n.260+8100A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-965759-A-G
• chr3-965759-A-T

Variant summary

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

The XR_001740585.2(LOC107986059):​n.260+8100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.945 in 151,922 control chromosomes in the GnomAD database, including 68,330 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 0.94 (68330 hom., cov: 30)
• Consequence: LOC107986059 XR_001740585.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 0 publications found

Genes affected

LOC107986059 (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 (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986059	XR_001740585.2	n.260+8100A>G		intron_variant	Intron 4 of 4
LOC107986059	XR_007095784.1	n.260+8100A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.945 AC: 143450 AN: 151802 Hom.: 68301 Cov.: 30

Gnomad AFR AF: 0.808

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.971

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.945 AC: 143535 AN: 151922 Hom.: 68330 Cov.: 30 AF XY: 0.946 AC XY: 70267 AN XY: 74240

African (AFR) AF: 0.808 AC: 33468 AN: 41420

American (AMR) AF: 0.980 AC: 14938 AN: 15238

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3466 AN: 3466

East Asian (EAS) AF: 1.00 AC: 5126 AN: 5126

South Asian (SAS) AF: 0.998 AC: 4806 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10598 AN: 10598

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67911 AN: 67944

Other (OTH) AF: 0.960 AC: 2026 AN: 2110

Alfa AF: 0.967 Hom.: 5487

Bravo AF: 0.938

Asia WGS AF: 0.983 AC: 3419 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	0.0030
DANN	Benign	0.42
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6803398; hg19: chr3-1007443;