rs690271

Variant names:

• chr15-53212475-G-A
• rs690271
• XR_004837531.2:n.481-8951G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_932257.3(LOC107983981):​n.697-8951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,158 control chromosomes in the GnomAD database, including 2,642 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 0.17 (2642 hom., cov: 32)
• Consequence: LOC107983981 XR_932257.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 2 publications found

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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: 0.165 AC: 25075 AN: 152040 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.165 AC: 25108 AN: 152158 Hom.: 2642 Cov.: 32 AF XY: 0.165 AC XY: 12287 AN XY: 74378

African (AFR) AF: 0.253 AC: 10484 AN: 41480

American (AMR) AF: 0.167 AC: 2551 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3472

East Asian (EAS) AF: 0.415 AC: 2147 AN: 5176

South Asian (SAS) AF: 0.220 AC: 1063 AN: 4828

European-Finnish (FIN) AF: 0.0574 AC: 609 AN: 10602

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7113 AN: 68000

Other (OTH) AF: 0.171 AC: 360 AN: 2110

Alfa AF: 0.138 Hom.: 305

Bravo AF: 0.180

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	17
DANN	Benign	0.76
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs690271; hg19: chr15-53504672;