XR_007059886.1:n.1639G>A

Variant names:

• chr6-168686862-G-A
• rs611525
• XR_007059886.1:n.1639G>A

Variant summary

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

The XR_007059886.1(LOC124901468):​n.1639G>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 0.955 in 152,310 control chromosomes in the GnomAD database, including 69,521 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 0.96 (69521 hom., cov: 33)
• Consequence: LOC124901468 XR_007059886.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 4 publications found

Genes affected

LOC124901468 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 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: 0.955 AC: 145381 AN: 152192 Hom.: 69476 Cov.: 33

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.955 AC: 145486 AN: 152310 Hom.: 69521 Cov.: 33 AF XY: 0.954 AC XY: 71019 AN XY: 74458

African (AFR) AF: 0.980 AC: 40732 AN: 41582

American (AMR) AF: 0.927 AC: 14184 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3311 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4968 AN: 5168

South Asian (SAS) AF: 0.966 AC: 4664 AN: 4830

European-Finnish (FIN) AF: 0.931 AC: 9881 AN: 10608

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64534 AN: 68036

Other (OTH) AF: 0.956 AC: 2023 AN: 2116

Alfa AF: 0.951 Hom.: 11160

Bravo AF: 0.957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs611525; hg19: chr6-169086978;