rs1560547

chr4-186850554-A-G

Variant summary

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

The XR_007058501.1(LOC102723906):n.328+9565A>G 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 0.874 in 152,120 control chromosomes in the GnomAD database, including 58,191 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 0.87 (58191 hom., cov: 31)
• Consequence: LOC102723906 XR_007058501.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

Genes affected

LOC102723906 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723906	XR_007058501.1	n.328+9565A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132779 AN: 152002 Hom.: 58139 Cov.: 31

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.874 AC: 132889 AN: 152120 Hom.: 58191 Cov.: 31 AF XY: 0.876 AC XY: 65119 AN XY: 74368

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.884

Alfa AF: 0.885 Hom.: 42051

Bravo AF: 0.866

Asia WGS AF: 0.945 AC: 3286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.78
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1560547; hg19: chr4-187771708;