chr6-43797617-A-C

Position:

• chr6-43797617-A-C

Variant summary

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

The XR_007059588.1(LOC105375070):​n.192+267A>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 0.39 in 152,136 control chromosomes in the GnomAD database, including 15,315 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 0.39 (15315 hom., cov: 33)
• Consequence: LOC105375070 XR_007059588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

LOC105375070 (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 (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375070	XR_007059588.1	n.192+267A>C		intron_variant, non_coding_transcript_variant
POLR1C	NM_001318876.2	c.945+268346A>C		intron_variant
LOC105375070	XR_007059589.1	n.192+267A>C		intron_variant, non_coding_transcript_variant
LOC105375070	XR_926833.3	n.192+267A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59267 AN: 152018 Hom.: 15270 Cov.: 33

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.390 AC: 59359 AN: 152136 Hom.: 15315 Cov.: 33 AF XY: 0.382 AC XY: 28389 AN XY: 74390

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.373

Alfa AF: 0.257 Hom.: 2952

Bravo AF: 0.407

Asia WGS AF: 0.344 AC: 1197 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	1.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885658; hg19: chr6-43765354;