rs6728853

Variant names:

• chr2-220066856-C-T
• rs6728853
• ENST00000830324.1:n.467-2307C>T

Variant summary

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

The ENST00000830324.1(ENSG00000288902):​n.467-2307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,176 control chromosomes in the GnomAD database, including 38,960 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 0.72 (38960 hom., cov: 33)
• Consequence: ENSG00000288902 ENST00000830324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 0 publications found

Genes affected

ENSG00000288902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.771 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
ENSG00000288902	ENST00000830324.1	n.467-2307C>T		intron_variant	Intron 2 of 5
ENSG00000288902	ENST00000830326.1	n.256-2307C>T		intron_variant	Intron 2 of 4
ENSG00000288902	ENST00000830327.1	n.842-2307C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108832 AN: 152058 Hom.: 38932 Cov.: 33

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.716 AC: 108905 AN: 152176 Hom.: 38960 Cov.: 33 AF XY: 0.717 AC XY: 53337 AN XY: 74378

African (AFR) AF: 0.737 AC: 30578 AN: 41516

American (AMR) AF: 0.676 AC: 10337 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2797 AN: 3472

East Asian (EAS) AF: 0.757 AC: 3925 AN: 5184

South Asian (SAS) AF: 0.792 AC: 3820 AN: 4824

European-Finnish (FIN) AF: 0.725 AC: 7673 AN: 10582

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47459 AN: 67996

Other (OTH) AF: 0.711 AC: 1505 AN: 2116

Alfa AF: 0.707 Hom.: 43157

Bravo AF: 0.715

Asia WGS AF: 0.777 AC: 2701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.79
DANN	Benign	0.43
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6728853; hg19: chr2-220931577;