rs4848143

chr2-121054648-A-G

Variant summary

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

The XR_923264.2(LOC105373587):n.1030-1739A>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 0.51 in 151,944 control chromosomes in the GnomAD database, including 23,653 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 0.51 (23653 hom., cov: 30)
• Consequence: LOC105373587 XR_923264.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

LOC105373587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373587	XR_923264.2	n.1030-1739A>G		intron_variant, non_coding_transcript_variant
LOC105373587	XR_923265.2	n.230-1739A>G		intron_variant, non_coding_transcript_variant
LOC105373587	XR_923266.2	n.1030-1806A>G		intron_variant, non_coding_transcript_variant
LOC105373587	XR_923267.2	n.202-1739A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77485 AN: 151826 Hom.: 23648 Cov.: 30

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.510 AC: 77487 AN: 151944 Hom.: 23653 Cov.: 30 AF XY: 0.511 AC XY: 37939 AN XY: 74250

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.551

Alfa AF: 0.620 Hom.: 13744

Bravo AF: 0.487

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4848143; hg19: chr2-121812224;