6-164010016-C-T

Position:

• chr6-164010016-C-T

Variant summary

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

The XR_943213.4(LOC105378102):​n.559-47032C>T 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 0.798 in 152,020 control chromosomes in the GnomAD database, including 48,431 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 (48431 hom., cov: 31)
• Consequence: LOC105378102 XR_943213.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

Genes affected

LOC105378102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378102	XR_943213.4	n.559-47032C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659063.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121147 AN: 151902 Hom.: 48368 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.798 AC: 121271 AN: 152020 Hom.: 48431 Cov.: 31 AF XY: 0.801 AC XY: 59540 AN XY: 74318

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.788

Alfa AF: 0.795 Hom.: 7780

Bravo AF: 0.802

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs206012; hg19: chr6-164431048;