rs12118986

Positions:

• chr1-61638142-C-A
• chr1-61638142-C-G

Variant summary

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

The XR_001738095.3(LOC107984964):​n.109+834C>A 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 0.0399 in 152,198 control chromosomes in the GnomAD database, including 196 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 0.040 (196 hom., cov: 32)
• Consequence: LOC107984964 XR_001738095.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496

Genes affected

LOC107984964 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984964	XR_001738095.3	n.109+834C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6073 AN: 152080 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.00961

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0399 AC: 6075 AN: 152198 Hom.: 196 Cov.: 32 AF XY: 0.0407 AC XY: 3026 AN XY: 74390

Gnomad4 AFR AF: 0.00959

Gnomad4 AMR AF: 0.0300

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0188

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0509 Hom.: 130

Bravo AF: 0.0329

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12118986; hg19: chr1-62103814;