6-168934803-C-T

Position:

• chr6-168934803-C-T

Variant summary

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

The NR_136250.1(LOC105378146):​n.385-6959G>A 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 0.878 in 151,586 control chromosomes in the GnomAD database, including 58,732 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 0.88 (58732 hom., cov: 30)
• Consequence: LOC105378146 NR_136250.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378146	NR_136250.1	n.385-6959G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669060.1	n.717-12700G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.878 AC: 132994 AN: 151466 Hom.: 58677 Cov.: 30

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.878 AC: 133106 AN: 151586 Hom.: 58732 Cov.: 30 AF XY: 0.878 AC XY: 64999 AN XY: 74056

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.897

Alfa AF: 0.911 Hom.: 66300

Bravo AF: 0.875

Asia WGS AF: 0.917 AC: 3093 AN: 3374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6455455; hg19: chr6-169334898;