rs350729

Variant names:

• chr2-52756635-T-G
• rs350729
• ENST00000421575.7:n.240-23858A>C

Variant summary

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

The ENST00000421575.7(ENSG00000228033):​n.240-23858A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,998 control chromosomes in the GnomAD database, including 32,803 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 0.65 (32803 hom., cov: 32)
• Consequence: ENSG00000228033 ENST00000421575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 12 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369165	NR_187747.1	n.172-29817A>C		intron_variant	Intron 3 of 4
LOC105369165	NR_187748.1	n.253-23858A>C		intron_variant	Intron 4 of 6
LOC105369165	NR_187749.1	n.221-29817A>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228033	ENST00000421575.7	n.240-23858A>C		intron_variant	Intron 3 of 5	5
ENSG00000228033	ENST00000443237.2	n.185-29817A>C		intron_variant	Intron 3 of 4	3
ENSG00000228033	ENST00000668945.1	n.220-29817A>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99347 AN: 151880 Hom.: 32792 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.654 AC: 99397 AN: 151998 Hom.: 32803 Cov.: 32 AF XY: 0.650 AC XY: 48275 AN XY: 74256

African (AFR) AF: 0.650 AC: 26948 AN: 41454

American (AMR) AF: 0.619 AC: 9438 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2398 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2394 AN: 5148

South Asian (SAS) AF: 0.585 AC: 2814 AN: 4812

European-Finnish (FIN) AF: 0.653 AC: 6912 AN: 10578

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45980 AN: 67962

Other (OTH) AF: 0.686 AC: 1450 AN: 2114

Alfa AF: 0.656 Hom.: 51265

Bravo AF: 0.651

Asia WGS AF: 0.548 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.22
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs350729; hg19: chr2-52983773;