rs891257

Variant names:

• chr2-5724337-C-G
• rs891257
• ENST00000829847.1:n.81+16030C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-5724337-C-G
• chr2-5724337-C-T

Variant summary

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

The ENST00000829847.1(ENSG00000236106):​n.81+16030C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,060 control chromosomes in the GnomAD database, including 14,562 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 0.44 (14562 hom., cov: 33)
• Consequence: ENSG00000236106 ENST00000829847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 1 publications found

Genes affected

ENSG00000236106 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 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
ENSG00000236106	ENST00000829847.1	n.81+16030C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66148 AN: 151942 Hom.: 14560 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.435 AC: 66186 AN: 152060 Hom.: 14562 Cov.: 33 AF XY: 0.438 AC XY: 32517 AN XY: 74320

African (AFR) AF: 0.447 AC: 18530 AN: 41484

American (AMR) AF: 0.528 AC: 8069 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3468

East Asian (EAS) AF: 0.483 AC: 2485 AN: 5150

South Asian (SAS) AF: 0.434 AC: 2095 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4111 AN: 10568

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

European-Non Finnish (NFE) AF: 0.415 AC: 28187 AN: 67960

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.299 Hom.: 724

Bravo AF: 0.448

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs891257; hg19: chr2-5864469;