rs4818677

Variant names:

• chr21-22418908-G-A
• rs4818677
• ENST00000444130.1:n.386-1862G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-22418908-G-A
• chr21-22418908-G-C
• chr21-22418908-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444130.1(ENSG00000226043):​n.386-1862G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 152,000 control chromosomes in the GnomAD database, including 64,254 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 0.92 (64254 hom., cov: 32)
• Consequence: ENSG00000226043 ENST00000444130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744

Genes affected

ENSG00000226043 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000226043	ENST00000444130.1	n.386-1862G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139402 AN: 151882 Hom.: 64219 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.929

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.918 AC: 139493 AN: 152000 Hom.: 64254 Cov.: 32 AF XY: 0.920 AC XY: 68372 AN XY: 74332

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.925

Alfa AF: 0.928 Hom.: 9323

Bravo AF: 0.914

Asia WGS AF: 0.958 AC: 3294 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4818677; hg19: chr21-23791228;