rs11835989

Variant names:

• chr12-91930977-T-C
• rs11835989
• ENST00000812104.1:n.180+7876T>C

Variant summary

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

The ENST00000812104.1(ENSG00000305639):​n.180+7876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,948 control chromosomes in the GnomAD database, including 16,016 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 (16016 hom., cov: 32)
• Consequence: ENSG00000305639 ENST00000812104.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 1 publications found

Genes affected

ENSG00000305639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812104.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305639	ENST00000812104.1		n.180+7876T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66561 AN: 151830 Hom.: 15981 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.439 AC: 66649 AN: 151948 Hom.: 16016 Cov.: 32 AF XY: 0.436 AC XY: 32375 AN XY: 74298

African (AFR) AF: 0.638 AC: 26453 AN: 41432

American (AMR) AF: 0.429 AC: 6556 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1145 AN: 3464

East Asian (EAS) AF: 0.109 AC: 561 AN: 5168

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4822

European-Finnish (FIN) AF: 0.353 AC: 3723 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24577 AN: 67918

Other (OTH) AF: 0.393 AC: 830 AN: 2114

Alfa AF: 0.422 Hom.: 2346

Bravo AF: 0.447

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11835989;

hg19: chr12-92324753;