6-164026979-A-G

Position:

• chr6-164026979-A-G

Variant summary

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

The XR_943213.4(LOC105378102):​n.559-30069A>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 0.669 in 152,080 control chromosomes in the GnomAD database, including 34,107 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 0.67 (34107 hom., cov: 33)
• Consequence: LOC105378102 XR_943213.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LOC105378102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378102	XR_943213.4	n.559-30069A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101597 AN: 151960 Hom.: 34054 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.669 AC: 101708 AN: 152080 Hom.: 34107 Cov.: 33 AF XY: 0.672 AC XY: 50007 AN XY: 74364

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.670

Alfa AF: 0.679 Hom.: 8979

Bravo AF: 0.671

Asia WGS AF: 0.774 AC: 2681 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.024
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs205990; hg19: chr6-164448011;