chr2-193119895-A-G

Variant names:

• chr2-193119895-A-G
• rs17662626
• XR_001739832.2:n.233+40425T>C

Variant summary

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

The XR_001739832.2(LOC107985969):​n.233+40425T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 152,138 control chromosomes in the GnomAD database, including 412 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 0.059 (412 hom., cov: 32)
• Consequence: LOC107985969 XR_001739832.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 37 publications found

Genes affected

LOC107985969 (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 = 0.138 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8979 AN: 152020 Hom.: 411 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0590 AC: 8974 AN: 152138 Hom.: 412 Cov.: 32 AF XY: 0.0594 AC XY: 4419 AN XY: 74374

African (AFR) AF: 0.0165 AC: 684 AN: 41532

American (AMR) AF: 0.143 AC: 2187 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0239 AC: 115 AN: 4820

European-Finnish (FIN) AF: 0.0601 AC: 638 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0758 AC: 5152 AN: 67968

Other (OTH) AF: 0.0550 AC: 116 AN: 2110

Alfa AF: 0.0701 Hom.: 1603

Bravo AF: 0.0633

Asia WGS AF: 0.0150 AC: 53 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.74
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs17662626; hg19: chr2-193984621;