1-202121513-C-G

Variant names:

• chr1-202121513-C-G
• rs4329563
• ENST00000723551.1:n.484-1563G>C

Variant summary

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

The ENST00000723551.1(ENSG00000294430):​n.484-1563G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,032 control chromosomes in the GnomAD database, including 14,059 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 0.42 (14059 hom., cov: 31)
• Consequence: ENSG00000294430 ENST00000723551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 4 publications found

Genes affected

ENSG00000294430 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294430	ENST00000723551.1	n.484-1563G>C		intron_variant	Intron 2 of 3
ENSG00000294430	ENST00000723552.1	n.192+1412G>C		intron_variant	Intron 1 of 2
ENSG00000294430	ENST00000723553.1	n.189+1412G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63911 AN: 151914 Hom.: 14056 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.0759

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.420 AC: 63928 AN: 152032 Hom.: 14059 Cov.: 31 AF XY: 0.421 AC XY: 31296 AN XY: 74306

African (AFR) AF: 0.360 AC: 14915 AN: 41476

American (AMR) AF: 0.407 AC: 6213 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3468

East Asian (EAS) AF: 0.0758 AC: 393 AN: 5182

South Asian (SAS) AF: 0.550 AC: 2651 AN: 4822

European-Finnish (FIN) AF: 0.455 AC: 4793 AN: 10544

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31511 AN: 67950

Other (OTH) AF: 0.430 AC: 910 AN: 2114

Alfa AF: 0.293 Hom.: 757

Bravo AF: 0.409

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4329563; hg19: chr1-202090641;