12-3935310-G-A

Variant names:

• chr12-3935310-G-A
• rs7133541
• ENST00000687881.2:n.163-11870C>T

Variant summary

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

The ENST00000687881.2(ENSG00000288729):​n.163-11870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 149,200 control chromosomes in the GnomAD database, including 11,680 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 0.36 (11680 hom., cov: 31)
• Consequence: ENSG00000288729 ENST00000687881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

Genes affected

ENSG00000288729 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687881.2. 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
	ENSG00000288729	ENST00000687881.2		n.163-11870C>T		intron	N/A
	ENSG00000288729	ENST00000690597.1		n.273-11870C>T		intron	N/A
	ENSG00000288729	ENST00000701907.2		n.165+21422C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 53853 AN: 149100 Hom.: 11658 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.361 AC: 53915 AN: 149200 Hom.: 11680 Cov.: 31 AF XY: 0.363 AC XY: 26433 AN XY: 72794

African (AFR) AF: 0.432 AC: 17218 AN: 39876

American (AMR) AF: 0.372 AC: 5484 AN: 14738

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1425 AN: 3458

East Asian (EAS) AF: 0.203 AC: 1009 AN: 4966

South Asian (SAS) AF: 0.434 AC: 2032 AN: 4678

European-Finnish (FIN) AF: 0.306 AC: 3203 AN: 10462

Middle Eastern (MID) AF: 0.545 AC: 158 AN: 290

European-Non Finnish (NFE) AF: 0.328 AC: 22211 AN: 67764

Other (OTH) AF: 0.397 AC: 818 AN: 2062

Alfa AF: 0.347 Hom.: 9041

Asia WGS AF: 0.409 AC: 1386 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.40
PhyloP100		-1.4

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: rs7133541;

hg19: chr12-4044476;