rs1599755

Variant names:

• chr2-195109639-C-T
• rs1599755
• XR_007088699.1:n.197-50136G>A

Variant summary

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

The XR_007088699.1(LOC105376755):​n.197-50136G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,078 control chromosomes in the GnomAD database, including 1,213 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 0.098 (1213 hom., cov: 32)
• Consequence: LOC105376755 XR_007088699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 2 publications found

Genes affected

LOC105376755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.0977 AC: 14839 AN: 151960 Hom.: 1213 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0838

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

GnomAD4 genome AF: 0.0977 AC: 14852 AN: 152078 Hom.: 1213 Cov.: 32 AF XY: 0.0951 AC XY: 7070 AN XY: 74340

African (AFR) AF: 0.228 AC: 9464 AN: 41454

American (AMR) AF: 0.0606 AC: 925 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0504 AC: 175 AN: 3472

East Asian (EAS) AF: 0.0599 AC: 310 AN: 5172

South Asian (SAS) AF: 0.0481 AC: 232 AN: 4826

European-Finnish (FIN) AF: 0.0403 AC: 427 AN: 10596

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3006 AN: 67988

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0614 Hom.: 2049

Bravo AF: 0.107

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1599755; hg19: chr2-195974363;