rs7530302

Variant names:

• chr1-220491610-G-A
• rs7530302
• XR_001737822.1:n.557-624G>A

Variant summary

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

The XR_922615.1(LOC105372928):​n.256-624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,084 control chromosomes in the GnomAD database, including 1,175 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 0.10 (1175 hom., cov: 32)
• Consequence: LOC105372928 XR_922615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 7 publications found

Genes affected

LOC105372928 (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 (AFR) allele frequency at 95% confidence interval = 0.205 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: 0.105 AC: 15893 AN: 151966 Hom.: 1166 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.105 AC: 15949 AN: 152084 Hom.: 1175 Cov.: 32 AF XY: 0.103 AC XY: 7672 AN XY: 74348

African (AFR) AF: 0.209 AC: 8655 AN: 41448

American (AMR) AF: 0.0593 AC: 906 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.109 AC: 565 AN: 5160

South Asian (SAS) AF: 0.150 AC: 720 AN: 4816

European-Finnish (FIN) AF: 0.0334 AC: 354 AN: 10596

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0591 AC: 4017 AN: 68010

Other (OTH) AF: 0.102 AC: 214 AN: 2102

Alfa AF: 0.0733 Hom.: 929

Bravo AF: 0.109

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.038
DANN	Benign	0.67
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7530302; hg19: chr1-220664952;