rs424950

Variant names:

• chr1-163987266-G-C
• rs424950
• ENST00000824604.1:n.44-2714G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000824604.1(ENSG00000307220):​n.44-2714G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,958 control chromosomes in the GnomAD database, including 13,100 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 0.40 (13100 hom., cov: 32)
• Consequence: ENSG00000307220 ENST00000824604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 6 publications found

Genes affected

ENSG00000307220 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 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
ENSG00000307220	ENST00000824604.1	n.44-2714G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60019 AN: 151842 Hom.: 13094 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.395 AC: 60046 AN: 151958 Hom.: 13100 Cov.: 32 AF XY: 0.398 AC XY: 29568 AN XY: 74270

African (AFR) AF: 0.198 AC: 8197 AN: 41458

American (AMR) AF: 0.392 AC: 5990 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3466

East Asian (EAS) AF: 0.413 AC: 2122 AN: 5138

South Asian (SAS) AF: 0.532 AC: 2565 AN: 4820

European-Finnish (FIN) AF: 0.507 AC: 5347 AN: 10548

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32748 AN: 67944

Other (OTH) AF: 0.424 AC: 896 AN: 2112

Alfa AF: 0.431 Hom.: 1858

Bravo AF: 0.375

Asia WGS AF: 0.466 AC: 1620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	14
DANN	Benign	0.54
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs424950; hg19: chr1-163956503;