chr6-160120141-G-A

Variant names:

• chr6-160120141-G-A
• rs6935207
• XR_007059842.1:n.854+701C>T

Variant summary

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

The XR_007059842.1(LOC124901452):​n.854+701C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,106 control chromosomes in the GnomAD database, including 7,050 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 0.29 (7050 hom., cov: 33)
• Consequence: LOC124901452 XR_007059842.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 8 publications found

Genes affected

LOC124901452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44273 AN: 151988 Hom.: 7030 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.292 AC: 44347 AN: 152106 Hom.: 7050 Cov.: 33 AF XY: 0.293 AC XY: 21757 AN XY: 74372

African (AFR) AF: 0.401 AC: 16619 AN: 41444

American (AMR) AF: 0.315 AC: 4819 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2684 AN: 5178

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2357 AN: 10596

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15334 AN: 68002

Other (OTH) AF: 0.272 AC: 572 AN: 2104

Alfa AF: 0.244 Hom.: 1436

Bravo AF: 0.307

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.57
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs6935207; hg19: chr6-160541173;