rs17089462

Positions:

• chr13-64645041-G-A
• chr13-64645041-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001750010.1(LOC107987190):​n.84+722G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,150 control chromosomes in the GnomAD database, including 532 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 0.075 (532 hom., cov: 32)
• Consequence: LOC107987190 XR_001750010.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

Genes affected

LOC107987190 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987190	XR_001750010.1	n.84+722G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11455 AN: 152032 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0180

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0836

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

GnomAD4 genome AF: 0.0754 AC: 11473 AN: 152150 Hom.: 532 Cov.: 32 AF XY: 0.0746 AC XY: 5549 AN XY: 74376

Gnomad4 AFR AF: 0.0330

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0884

Alfa AF: 0.0372 Hom.: 41

Bravo AF: 0.0684

Asia WGS AF: 0.100 AC: 347 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.60
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17089462; hg19: chr13-65219173; COSMIC: COSV60729873;