18-71581359-T-C

Variant summary

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

The XR_001753502.1(LOC107985179):n.149+33304T>C 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 0.862 in 152,102 control chromosomes in the GnomAD database, including 56,670 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 0.86 (56670 hom., cov: 32)
• Consequence: LOC107985179 XR_001753502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

LOC107985179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985179	XR_001753502.1	n.149+33304T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131055 AN: 151984 Hom.: 56664 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.862 AC: 131109 AN: 152102 Hom.: 56670 Cov.: 32 AF XY: 0.861 AC XY: 64037 AN XY: 74342

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.868

Alfa AF: 0.891 Hom.: 122196

Bravo AF: 0.857

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.23
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1539909; hg19: chr18-69248595;