6-66060161-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377840	XR_942656.2	n.122C>A		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105377840	XR_942654.2	n.62+133C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309260	ENST00000839883.1	n.343+1791G>T		intron_variant	Intron 3 of 6
ENSG00000309260	ENST00000839884.1	n.106+1791G>T		intron_variant	Intron 2 of 4
ENSG00000309275	ENST00000839997.1	n.47+133C>A		intron_variant	Intron 1 of 3
ENSG00000309275	ENST00000839998.1	n.42+133C>A		intron_variant	Intron 1 of 2

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 v4.3

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;