rs17063114

Variant names:

• chr4-176480299-G-A
• rs17063114
• XR_007058376.1:n.1157+29475G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-176480299-G-A
• chr4-176480299-G-C
• chr4-176480299-G-T

Variant summary

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

The XR_007058376.1(LOC124900817):​n.1157+29475G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,024 control chromosomes in the GnomAD database, including 10,352 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 0.36 (10352 hom., cov: 32)
• Consequence: LOC124900817 XR_007058376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

Genes affected

LOC124900817 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900817	XR_007058376.1	n.1157+29475G>A		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55206 AN: 151906 Hom.: 10344 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.363 AC: 55235 AN: 152024 Hom.: 10352 Cov.: 32 AF XY: 0.361 AC XY: 26848 AN XY: 74310

African (AFR) AF: 0.423 AC: 17512 AN: 41448

American (AMR) AF: 0.384 AC: 5860 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3470

East Asian (EAS) AF: 0.133 AC: 687 AN: 5176

South Asian (SAS) AF: 0.319 AC: 1535 AN: 4814

European-Finnish (FIN) AF: 0.336 AC: 3553 AN: 10570

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23690 AN: 67968

Other (OTH) AF: 0.374 AC: 787 AN: 2106

Alfa AF: 0.326 Hom.: 3313

Bravo AF: 0.364

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17063114; hg19: chr4-177401450;