rs2424635

Variant names:

• chr20-24736449-C-A
• rs2424635
• ENST00000755080.1:n.154-3520G>T

Variant summary

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

The ENST00000755080.1(ENSG00000298359):​n.154-3520G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,190 control chromosomes in the GnomAD database, including 22,103 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 0.52 (22103 hom., cov: 34)
• Consequence: ENSG00000298359 ENST00000755080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 5 publications found

Genes affected

ENSG00000298359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755080.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298359	ENST00000755080.1		n.154-3520G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79191 AN: 152072 Hom.: 22109 Cov.: 34

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.520 AC: 79203 AN: 152190 Hom.: 22103 Cov.: 34 AF XY: 0.519 AC XY: 38619 AN XY: 74410

African (AFR) AF: 0.378 AC: 15708 AN: 41520

American (AMR) AF: 0.485 AC: 7417 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2251 AN: 3470

East Asian (EAS) AF: 0.139 AC: 717 AN: 5170

South Asian (SAS) AF: 0.463 AC: 2237 AN: 4828

European-Finnish (FIN) AF: 0.662 AC: 7010 AN: 10586

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41970 AN: 68008

Other (OTH) AF: 0.512 AC: 1080 AN: 2110

Alfa AF: 0.503 Hom.: 8167

Bravo AF: 0.498

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.76
PhyloP100		-0.24

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2424635;

hg19: chr20-24717085;