rs768352

Variant names:

• chr2-184464964-G-A
• rs768352
• XR_923656.1:n.233-1260G>A

Variant summary

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

The XR_923656.1(LOC105373779):​n.233-1260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,894 control chromosomes in the GnomAD database, including 10,933 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 0.35 (10933 hom., cov: 31)
• Consequence: LOC105373779 XR_923656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 0 publications found

Genes affected

LOC105373779 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 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: 0.348 AC: 52809 AN: 151774 Hom.: 10937 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.348 AC: 52804 AN: 151894 Hom.: 10933 Cov.: 31 AF XY: 0.342 AC XY: 25363 AN XY: 74244

African (AFR) AF: 0.148 AC: 6159 AN: 41486

American (AMR) AF: 0.379 AC: 5780 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3464

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5168

South Asian (SAS) AF: 0.371 AC: 1784 AN: 4810

European-Finnish (FIN) AF: 0.345 AC: 3624 AN: 10492

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32183 AN: 67918

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.403 Hom.: 1647

Bravo AF: 0.341

Asia WGS AF: 0.199 AC: 691 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.13
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs768352; hg19: chr2-185329691;