rs7597224

Variant names:

• chr2-18784356-C-A
• rs7597224
• XR_001739304.3:n.973+96028C>A

Variant summary

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

The XR_001739304.3(LOC105373456):​n.973+96028C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,022 control chromosomes in the GnomAD database, including 9,086 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 0.34 (9086 hom., cov: 32)
• Consequence: LOC105373456 XR_001739304.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

Genes affected

LOC105373456 (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 (NFE) allele frequency at 95% confidence interval = 0.388 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: 0.336 AC: 50997 AN: 151904 Hom.: 9082 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.336 AC: 51008 AN: 152022 Hom.: 9086 Cov.: 32 AF XY: 0.336 AC XY: 24974 AN XY: 74298

African (AFR) AF: 0.232 AC: 9629 AN: 41480

American (AMR) AF: 0.320 AC: 4885 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1367 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5156

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4818

European-Finnish (FIN) AF: 0.390 AC: 4119 AN: 10554

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26633 AN: 67956

Other (OTH) AF: 0.341 AC: 720 AN: 2112

Alfa AF: 0.374 Hom.: 5674

Bravo AF: 0.326

Asia WGS AF: 0.303 AC: 1054 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	3.3
DANN	Benign	0.66
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7597224; hg19: chr2-18965622;