rs1885659

chr6-43797796-A-Gchr6-43797796-A-T

Variant summary

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

The XR_007059588.1(LOC105375070):n.192+446A>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 0.801 in 152,266 control chromosomes in the GnomAD database, including 49,329 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 0.80 (49329 hom., cov: 34)
• Consequence: LOC105375070 XR_007059588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LOC105375070 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375070	XR_007059588.1	n.192+446A>G		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+268525A>G		intron_variant
LOC105375070	XR_007059589.1	n.192+446A>G		intron_variant, non_coding_transcript_variant
LOC105375070	XR_926833.3	n.192+446A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121772 AN: 152148 Hom.: 49265 Cov.: 34

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.801 AC: 121897 AN: 152266 Hom.: 49329 Cov.: 34 AF XY: 0.800 AC XY: 59594 AN XY: 74452

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.798

Alfa AF: 0.758 Hom.: 38923

Bravo AF: 0.803

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885659; hg19: chr6-43765533;