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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986098	XR_001740754.1	n.239-61262G>A		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;