rs2420900

Variant names:

• chr10-121069161-T-C
• rs2420900
• ENST00000824719.1:n.197-4993A>G

Variant summary

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

The ENST00000824719.1(ENSG00000307246):​n.197-4993A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,998 control chromosomes in the GnomAD database, including 15,450 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 0.44 (15450 hom., cov: 31)
• Consequence: ENSG00000307246 ENST00000824719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 2 publications found

Genes affected

ENSG00000307246 (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 = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378521	XR_001747610.2	n.194-4993A>G		intron_variant	Intron 2 of 2
LOC105378521	XR_001747611.2	n.194-4993A>G		intron_variant	Intron 2 of 3
LOC105378521	XR_001747612.2	n.189-4993A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307246	ENST00000824719.1	n.197-4993A>G		intron_variant	Intron 2 of 3
ENSG00000307261	ENST00000824810.1	n.221-656T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66728 AN: 151880 Hom.: 15414 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.440 AC: 66823 AN: 151998 Hom.: 15450 Cov.: 31 AF XY: 0.443 AC XY: 32903 AN XY: 74292

African (AFR) AF: 0.581 AC: 24074 AN: 41438

American (AMR) AF: 0.440 AC: 6726 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1633 AN: 5158

South Asian (SAS) AF: 0.424 AC: 2032 AN: 4794

European-Finnish (FIN) AF: 0.455 AC: 4817 AN: 10580

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24781 AN: 67962

Other (OTH) AF: 0.438 AC: 925 AN: 2114

Alfa AF: 0.388 Hom.: 6176

Bravo AF: 0.441

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.43
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2420900; hg19: chr10-122828674;