rs622199

Variant names:

• chr3-73256146-G-A
• rs622199
• XR_001740754.1:n.239-61262G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-73256146-G-A
• chr3-73256146-G-C

Variant summary

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

The XR_001740754.1(LOC107986098):​n.239-61262G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,346 control chromosomes in the GnomAD database, including 69,797 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 0.96 (69797 hom., cov: 33)
• Consequence: LOC107986098 XR_001740754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 0 publications found

Genes affected

LOC107986098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145675 AN: 152228 Hom.: 69742 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.957 AC: 145789 AN: 152346 Hom.: 69797 Cov.: 33 AF XY: 0.957 AC XY: 71312 AN XY: 74498

African (AFR) AF: 0.928 AC: 38572 AN: 41574

American (AMR) AF: 0.980 AC: 14995 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3359 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4928 AN: 5186

South Asian (SAS) AF: 0.987 AC: 4768 AN: 4832

European-Finnish (FIN) AF: 0.963 AC: 10223 AN: 10618

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65785 AN: 68040

Other (OTH) AF: 0.954 AC: 2014 AN: 2112

Alfa AF: 0.961 Hom.: 107744

Bravo AF: 0.957

Asia WGS AF: 0.964 AC: 3353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs622199; hg19: chr3-73305297;