chr6-82674927-A-G

Variant names:

• chr6-82674927-A-G
• rs2482403
• XR_001744232.2:n.702+2212T>C

Variant summary

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

The XR_942739.2(LOC105377876):​n.566+2212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,896 control chromosomes in the GnomAD database, including 36,734 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 0.69 (36734 hom., cov: 32)
• Consequence: LOC105377876 XR_942739.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 0 publications found

Genes affected

LOC105377876 (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 (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104775 AN: 151778 Hom.: 36700 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.690 AC: 104856 AN: 151896 Hom.: 36734 Cov.: 32 AF XY: 0.693 AC XY: 51433 AN XY: 74248

African (AFR) AF: 0.789 AC: 32698 AN: 41450

American (AMR) AF: 0.716 AC: 10905 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2573 AN: 3466

East Asian (EAS) AF: 0.898 AC: 4633 AN: 5158

South Asian (SAS) AF: 0.719 AC: 3464 AN: 4820

European-Finnish (FIN) AF: 0.611 AC: 6456 AN: 10568

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 41936 AN: 67898

Other (OTH) AF: 0.685 AC: 1441 AN: 2104

Alfa AF: 0.675 Hom.: 5223

Bravo AF: 0.705

Asia WGS AF: 0.788 AC: 2741 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.55
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2482403; hg19: chr6-83384644;