XR_001745121.2:n.209+25366C>A

Variant names:

• chr7-24293991-G-T
• rs16474
• XR_001745121.2:n.209+25366C>A

Variant summary

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

The XR_001745121.2(LOC107986777):​n.209+25366C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,912 control chromosomes in the GnomAD database, including 19,685 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 0.50 (19685 hom., cov: 32)
• Consequence: LOC107986777 XR_001745121.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+25366C>A		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-96962C>A		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+25366C>A		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76475 AN: 151794 Hom.: 19675 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.504 AC: 76523 AN: 151912 Hom.: 19685 Cov.: 32 AF XY: 0.509 AC XY: 37763 AN XY: 74222

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.507

Alfa AF: 0.380 Hom.: 1042

Bravo AF: 0.507

Asia WGS AF: 0.564 AC: 1959 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16474; hg19: chr7-24333610;