6-84353108-C-T

Position:

• chr6-84353108-C-T

Variant summary

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

The XR_001744235.2(LOC107986620):​n.130+187C>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 0.757 in 151,966 control chromosomes in the GnomAD database, including 44,020 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 0.76 (44020 hom., cov: 31)
• Consequence: LOC107986620 XR_001744235.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

LOC107986620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986620	XR_001744235.2	n.130+187C>T		intron_variant, non_coding_transcript_variant
LOC107986621	XR_001744237.1	n.28-275G>A		intron_variant, non_coding_transcript_variant
LOC107986620	XR_001744236.1	n.73+187C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114954 AN: 151848 Hom.: 43984 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.757 AC: 115042 AN: 151966 Hom.: 44020 Cov.: 31 AF XY: 0.762 AC XY: 56583 AN XY: 74266

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.781

Alfa AF: 0.777 Hom.: 43626

Bravo AF: 0.750

Asia WGS AF: 0.885 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6928921; hg19: chr6-85062826;