13-64645041-G-A

Variant names:

• chr13-64645041-G-A
• rs17089462
• XR_001750010.1:n.84+722G>A

Variant summary

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

The XR_001750010.1(LOC107987190):​n.84+722G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 0 publications found

Genes affected

LOC107987190 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107987190	XR_001750010.1	n.84+722G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0330 AC: 1369 AN: 41532

American (AMR) AF: 0.0592 AC: 904 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 352 AN: 3466

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5162

South Asian (SAS) AF: 0.144 AC: 694 AN: 4826

European-Finnish (FIN) AF: 0.0923 AC: 977 AN: 10582

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6798 AN: 67988

Other (OTH) AF: 0.0884 AC: 187 AN: 2116

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

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