XR_942656.2:n.122C>A

Variant names:

• chr6-66060161-G-T
• rs207078
• XR_942656.2:n.122C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_942656.2(LOC105377840):​n.122C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,772 control chromosomes in the GnomAD database, including 32,718 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 0.65 (32718 hom., cov: 32)
• Consequence: LOC105377840 XR_942656.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

LOC105377840 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839883.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309260	ENST00000839883.1		n.343+1791G>T		intron	N/A
	ENSG00000309260	ENST00000839884.1		n.106+1791G>T		intron	N/A
	ENSG00000309275	ENST00000839997.1		n.47+133C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98108 AN: 151652 Hom.: 32681 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.647 AC: 98200 AN: 151772 Hom.: 32718 Cov.: 32 AF XY: 0.652 AC XY: 48334 AN XY: 74160

African (AFR) AF: 0.814 AC: 33697 AN: 41400

American (AMR) AF: 0.649 AC: 9865 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1868 AN: 3470

East Asian (EAS) AF: 0.788 AC: 4063 AN: 5156

South Asian (SAS) AF: 0.675 AC: 3258 AN: 4826

European-Finnish (FIN) AF: 0.611 AC: 6444 AN: 10540

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 36997 AN: 67868

Other (OTH) AF: 0.626 AC: 1318 AN: 2104

Alfa AF: 0.611 Hom.: 4907

Bravo AF: 0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.67
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs207078; hg19: chr6-66770054;