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_004837531.2(LOC107983981):​n.481-8951G>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_004837531.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837531.2	n.481-8951G>A		intron_variant	Intron 4 of 4
LOC107983981	XR_932257.3	n.697-8951G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;