rs1362858

Positions:

• chr18-35406636-C-A
• chr18-35406636-C-G

Variant summary

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

The XR_935376.3(LOC105372063):​n.402+2037G>T 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 0.707 in 152,076 control chromosomes in the GnomAD database, including 38,069 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 0.71 (38069 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC105372063 XR_935376.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

LOC105372063 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372063	XR_935376.3	n.402+2037G>T		intron_variant, non_coding_transcript_variant
LOC105372063	XR_007066338.1	n.2171G>T		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107491 AN: 151958 Hom.: 38039 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.707 AC: 107575 AN: 152076 Hom.: 38069 Cov.: 32 AF XY: 0.708 AC XY: 52633 AN XY: 74354

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.687

Alfa AF: 0.706 Hom.: 57030

Bravo AF: 0.712

Asia WGS AF: 0.730 AC: 2538 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362858; hg19: chr18-32986600;