rs1510107

Variant names:

• chr2-52932999-C-G
• rs1510107
• ENST00000421575.7:n.117-22975G>C

Variant summary

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

The ENST00000421575.7(ENSG00000228033):​n.117-22975G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,758 control chromosomes in the GnomAD database, including 40,158 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 0.71 (40158 hom., cov: 30)
• Consequence: ENSG00000228033 ENST00000421575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10
• Publications: 6 publications found

Genes affected

ENSG00000228033 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369165	NR_187747.1	n.49-22975G>C		intron_variant	Intron 1 of 4
LOC105369165	NR_187748.1	n.49-22975G>C		intron_variant	Intron 1 of 6
LOC105369165	NR_187749.1	n.97+1406G>C		intron_variant	Intron 1 of 5
LOC105369165	NR_187750.1	n.49-22975G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228033	ENST00000421575.7	n.117-22975G>C		intron_variant	Intron 1 of 5	5
ENSG00000228033	ENST00000443237.2	n.61+10476G>C		intron_variant	Intron 1 of 4	3
ENSG00000228033	ENST00000668945.1	n.96+1406G>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108230 AN: 151640 Hom.: 40093 Cov.: 30

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.714 AC: 108361 AN: 151758 Hom.: 40158 Cov.: 30 AF XY: 0.712 AC XY: 52784 AN XY: 74100

African (AFR) AF: 0.920 AC: 38150 AN: 41474

American (AMR) AF: 0.648 AC: 9860 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2105 AN: 3472

East Asian (EAS) AF: 0.432 AC: 2209 AN: 5114

South Asian (SAS) AF: 0.804 AC: 3865 AN: 4810

European-Finnish (FIN) AF: 0.680 AC: 7140 AN: 10504

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43006 AN: 67852

Other (OTH) AF: 0.670 AC: 1415 AN: 2112

Alfa AF: 0.704 Hom.: 4766

Bravo AF: 0.713

Asia WGS AF: 0.685 AC: 2379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.041
DANN	Benign	0.58
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs1510107; hg19: chr2-53160137;