1-118841195-T-C

Position:

• chr1-118841195-T-C

Variant summary

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

The XR_001737805.1(LOC107985447):​n.429+24679A>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 0.354 in 151,854 control chromosomes in the GnomAD database, including 9,581 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 0.35 (9581 hom., cov: 31)
• Consequence: LOC107985447 XR_001737805.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779

Genes affected

LOC107985447 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985447	XR_001737805.1	n.429+24679A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53656 AN: 151736 Hom.: 9568 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.354 AC: 53692 AN: 151854 Hom.: 9581 Cov.: 31 AF XY: 0.353 AC XY: 26226 AN XY: 74216

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.354

Alfa AF: 0.363 Hom.: 19543

Bravo AF: 0.349

Asia WGS AF: 0.280 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
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: rs1766803; hg19: chr1-119383818;