rs2821557

Variant names:

• chr1-110676298-C-T
• rs2821557
• ENST00000768410.1:n.218+35773C>T

Variant summary

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

The ENST00000768410.1(ENSG00000300042):​n.218+35773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,048 control chromosomes in the GnomAD database, including 27,878 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 0.60 (27878 hom., cov: 32)
• Consequence: ENSG00000300042 ENST00000768410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 11 publications found

Genes affected

ENSG00000300042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 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
ENSG00000300042	ENST00000768410.1	n.218+35773C>T		intron_variant	Intron 1 of 1
ENSG00000300042	ENST00000768411.1	n.208-18098C>T		intron_variant	Intron 1 of 2
ENSG00000300042	ENST00000768412.1	n.241-16136C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91255 AN: 151930 Hom.: 27843 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.601 AC: 91347 AN: 152048 Hom.: 27878 Cov.: 32 AF XY: 0.598 AC XY: 44466 AN XY: 74308

African (AFR) AF: 0.714 AC: 29616 AN: 41456

American (AMR) AF: 0.592 AC: 9056 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2273 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2188 AN: 5172

South Asian (SAS) AF: 0.440 AC: 2126 AN: 4832

European-Finnish (FIN) AF: 0.577 AC: 6099 AN: 10562

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 38003 AN: 67956

Other (OTH) AF: 0.635 AC: 1342 AN: 2112

Alfa AF: 0.579 Hom.: 100602

Bravo AF: 0.610

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.51
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs2821557; hg19: chr1-111218920;