rs4663105

Positions:

• chr2-127133851-A-C

Variant summary

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

The XR_923311.4(LOC105373605):​n.910+549A>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 0.463 in 151,642 control chromosomes in the GnomAD database, including 16,715 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 0.46 (16715 hom., cov: 30)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373605	XR_923311.4	n.910+549A>C		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3	n.513+549A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70057 AN: 151522 Hom.: 16652 Cov.: 30

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.463 AC: 70188 AN: 151642 Hom.: 16715 Cov.: 30 AF XY: 0.462 AC XY: 34258 AN XY: 74108

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.425

Alfa AF: 0.443 Hom.: 1906

Bravo AF: 0.470

Asia WGS AF: 0.539 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4663105; hg19: chr2-127891427;