rs1856748

Positions:

• chr1-206894495-T-C

Variant summary

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

The XR_007066836.1(LOC105372879):​n.125+1499A>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 0.468 in 150,382 control chromosomes in the GnomAD database, including 16,821 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 0.47 (16821 hom., cov: 31)
• Consequence: LOC105372879 XR_007066836.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

Genes affected

LOC105372879 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372879	XR_007066836.1	n.125+1499A>G		intron_variant, non_coding_transcript_variant
LOC105372879	XR_007066835.1	n.125+1499A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70344 AN: 150266 Hom.: 16805 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.468 AC: 70415 AN: 150382 Hom.: 16821 Cov.: 31 AF XY: 0.459 AC XY: 33768 AN XY: 73536

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.494

Alfa AF: 0.461 Hom.: 3345

Bravo AF: 0.477

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1856748; hg19: chr1-207067840;