rs2482403

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_001744232.2(LOC105377876):​n.702+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_001744232.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377876	XR_001744232.2	n.702+2212T>C		intron_variant	Intron 5 of 5
LOC105377876	XR_942739.2	n.566+2212T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;