rs871880

Variant names:

• chr12-43331201-A-T
• rs871880
• ENST00000810541.1:n.132+24875A>T

Variant summary

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

The ENST00000810541.1(ENSG00000305349):​n.132+24875A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,850 control chromosomes in the GnomAD database, including 19,199 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 0.49 (19199 hom., cov: 31)
• Consequence: ENSG00000305349 ENST00000810541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 2 publications found

Genes affected

ENSG00000305349 (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 (EAS) allele frequency at 95% confidence interval = 0.868 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
ENSG00000305349	ENST00000810541.1	n.132+24875A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74775 AN: 151732 Hom.: 19179 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.493 AC: 74847 AN: 151850 Hom.: 19199 Cov.: 31 AF XY: 0.498 AC XY: 36999 AN XY: 74226

African (AFR) AF: 0.473 AC: 19558 AN: 41370

American (AMR) AF: 0.583 AC: 8901 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3464

East Asian (EAS) AF: 0.890 AC: 4595 AN: 5164

South Asian (SAS) AF: 0.644 AC: 3108 AN: 4826

European-Finnish (FIN) AF: 0.408 AC: 4278 AN: 10492

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31057 AN: 67958

Other (OTH) AF: 0.529 AC: 1114 AN: 2106

Alfa AF: 0.454 Hom.: 1991

Bravo AF: 0.507

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.84
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs871880; hg19: chr12-43725004;